TY  - JOUR
AU  - Novković, Mirjana
AU  - Banović Đeri, Bojana
AU  - RistivojeviĆ, Bojan
AU  - Knežević, Aleksandra
AU  - Janković, Marko
AU  - Tanasić, Vanja
AU  - Radojičić, Verica
AU  - Keckarević, Dusan
AU  - Vidanović, Dejan
AU  - Tešović, Bojana
AU  - Skakić, Anita
AU  - Tolinački, Maja
AU  - Morić, Ivana
AU  - Đorđević, Valentina
PY  - 2024
UR  - https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1332276
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2327
AB  - The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has been evolving rapidly causing emergence of new variants and health uncertainties. Monitoring the evolution of the virus was of the utmost importance for public health interventions and the development of national and global mitigation strategies. Here, we report national data on the emergence of new variants, their distribution, and dynamics in a 3-year study conducted from March 2020 to the end of January 2023 in the Republic of Serbia. Nasopharyngeal and oropharyngeal swabs from 2,398 COVID-19-positive patients were collected and sequenced using three different next generation technologies: Oxford Nanopore, Ion Torrent, and DNBSeq. In the subset of 2,107 SARS-CoV-2 sequences which met the quality requirements, detection of mutations, assignment to SARS-CoV-2 lineages, and phylogenetic analysis were performed. During the 3-year period, we detected three variants of concern, namely, Alpha (5.6%), Delta (7.4%), and Omicron (70.3%) and one variant of interest—Omicron recombinant “Kraken” (XBB1.5) (<1%), whereas 16.8% of the samples belonged to other SARS-CoV-2 (sub)lineages. The detected SARS-CoV-2 (sub)lineages resulted in eight COVID-19 pandemic waves in Serbia, which correspond to the pandemic waves reported in Europe and the United States. Wave dynamics in Serbia showed the most resemblance with the profile of pandemic waves in southern Europe, consistent with the southeastern European location of Serbia. The samples were assigned to sixteen SARS-CoV-2 Nextstrain clades: 20A, 20B, 20C, 20D, 20E, 20G, 20I, 21J, 21K, 21L, 22A, 22B, 22C, 22D, 22E, and 22F and six different Omicron recombinants (XZ, XAZ, XAS, XBB, XBF, and XBK). The 10 most common mutations detected in the coding and untranslated regions of the SARS-CoV-2 genomes included four mutations affecting the spike protein (S:D614G, S:T478K, S:P681H, and S:S477N) and one mutation at each of the following positions: 5′-untranslated region (5’UTR:241); N protein (N:RG203KR); NSP3 protein (NSP3:F106F); NSP4 protein (NSP4:T492I); NSP6 protein (NSP6: S106/G107/F108 - triple deletion), and NSP12b protein (NSP12b:P314L). This national-level study is the most comprehensive in terms of sequencing and genomic surveillance of SARS-CoV-2 during the pandemic in Serbia, highlighting the importance of establishing and maintaining good national practice for monitoring SARS-CoV-2 and other viruses circulating worldwide.
AB  - The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has been evolving rapidly causing emergence of new variants and health uncertainties. Monitoring the evolution of the virus was of the utmost importance for public health interventions and the development of national and global mitigation strategies. Here, we report national data on the emergence of new variants, their distribution, and dynamics in a 3-year study conducted from March 2020 to the end of January 2023 in the Republic of Serbia. Nasopharyngeal and oropharyngeal swabs from 2,398 COVID-19- positive patients were collected and sequenced using three different next generation technologies: Oxford Nanopore, Ion Torrent, and DNBSeq. In the subset of 2,107 SARS-CoV-2 sequences which met the quality requirements, detection of mutations, assignment to SARS-CoV-2 lineages, and phylogenetic analysis were performed. During the 3-year period, we detected three variants of concern, namely, Alpha (5.6%), Delta (7.4%), and Omicron (70.3%) and one variant of interest—Omicron recombinant “Kraken” (XBB1.5) (<1%), whereas 16.8% of the samples belonged to other SARS-CoV-2 (sub)lineages. The detected SARS-CoV-2 (sub)lineages resulted in eight COVID-19 pandemic waves in Serbia, which correspond to the pandemic waves reported in Europe and the United States. Wave dynamics in Serbia showed the most resemblance with the profile of pandemic waves in southern Europe, consistent with the southeastern European location of Serbia. The samples were assigned to sixteen SARS-CoV-2 Nextstrain clades: 20A, 20B, 20C, 20D, 20E, 20G, 20I, 21J, 21K, 21L, 22A, 22B, 22C, 22D, 22E, and 22F and six different Omicron recombinants (XZ, XAZ, XAS, XBB, XBF, and XBK). The 10 most common mutations detected in the coding and untranslated regions of the SARS-CoV-2 genomes included four mutations affecting the spike protein (S:D614G, S:T478K, S:P681H, and S:S477N) and one mutation at each of the following positions: 5′-untranslated region (5’UTR:241); N protein (N:RG203KR); NSP3 protein (NSP3:F106F); NSP4 protein (NSP4:T492I); NSP6 protein (NSP6: S106/G107/F108 - triple deletion), and NSP12b protein (NSP12b:P314L). This national-level study is the most comprehensive in terms of sequencing and genomic surveillance of SARS-CoV-2 during the pandemic in Serbia, highlighting the importance of establishing and maintaining good national practice for monitoring SARS-CoV-2 and other viruses circulating worldwide.
PB  - Frontiers
T2  - Frontiers in Microbiology
T2  - Frontiers in Microbiology
T1  - Genome sequence diversity of SARS-CoV-2 in Serbia: insights gained from a 3-year pandemic study
VL  - 15
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2327
ER  - 

@article{
author = "Novković, Mirjana and Banović Đeri, Bojana and RistivojeviĆ, Bojan and Knežević, Aleksandra and Janković, Marko and Tanasić, Vanja and Radojičić, Verica and Keckarević, Dusan and Vidanović, Dejan and Tešović, Bojana and Skakić, Anita and Tolinački, Maja and Morić, Ivana and Đorđević, Valentina",
year = "2024",
abstract = "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has been evolving rapidly causing emergence of new variants and health uncertainties. Monitoring the evolution of the virus was of the utmost importance for public health interventions and the development of national and global mitigation strategies. Here, we report national data on the emergence of new variants, their distribution, and dynamics in a 3-year study conducted from March 2020 to the end of January 2023 in the Republic of Serbia. Nasopharyngeal and oropharyngeal swabs from 2,398 COVID-19-positive patients were collected and sequenced using three different next generation technologies: Oxford Nanopore, Ion Torrent, and DNBSeq. In the subset of 2,107 SARS-CoV-2 sequences which met the quality requirements, detection of mutations, assignment to SARS-CoV-2 lineages, and phylogenetic analysis were performed. During the 3-year period, we detected three variants of concern, namely, Alpha (5.6%), Delta (7.4%), and Omicron (70.3%) and one variant of interest—Omicron recombinant “Kraken” (XBB1.5) (<1%), whereas 16.8% of the samples belonged to other SARS-CoV-2 (sub)lineages. The detected SARS-CoV-2 (sub)lineages resulted in eight COVID-19 pandemic waves in Serbia, which correspond to the pandemic waves reported in Europe and the United States. Wave dynamics in Serbia showed the most resemblance with the profile of pandemic waves in southern Europe, consistent with the southeastern European location of Serbia. The samples were assigned to sixteen SARS-CoV-2 Nextstrain clades: 20A, 20B, 20C, 20D, 20E, 20G, 20I, 21J, 21K, 21L, 22A, 22B, 22C, 22D, 22E, and 22F and six different Omicron recombinants (XZ, XAZ, XAS, XBB, XBF, and XBK). The 10 most common mutations detected in the coding and untranslated regions of the SARS-CoV-2 genomes included four mutations affecting the spike protein (S:D614G, S:T478K, S:P681H, and S:S477N) and one mutation at each of the following positions: 5′-untranslated region (5’UTR:241); N protein (N:RG203KR); NSP3 protein (NSP3:F106F); NSP4 protein (NSP4:T492I); NSP6 protein (NSP6: S106/G107/F108 - triple deletion), and NSP12b protein (NSP12b:P314L). This national-level study is the most comprehensive in terms of sequencing and genomic surveillance of SARS-CoV-2 during the pandemic in Serbia, highlighting the importance of establishing and maintaining good national practice for monitoring SARS-CoV-2 and other viruses circulating worldwide., The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has been evolving rapidly causing emergence of new variants and health uncertainties. Monitoring the evolution of the virus was of the utmost importance for public health interventions and the development of national and global mitigation strategies. Here, we report national data on the emergence of new variants, their distribution, and dynamics in a 3-year study conducted from March 2020 to the end of January 2023 in the Republic of Serbia. Nasopharyngeal and oropharyngeal swabs from 2,398 COVID-19- positive patients were collected and sequenced using three different next generation technologies: Oxford Nanopore, Ion Torrent, and DNBSeq. In the subset of 2,107 SARS-CoV-2 sequences which met the quality requirements, detection of mutations, assignment to SARS-CoV-2 lineages, and phylogenetic analysis were performed. During the 3-year period, we detected three variants of concern, namely, Alpha (5.6%), Delta (7.4%), and Omicron (70.3%) and one variant of interest—Omicron recombinant “Kraken” (XBB1.5) (<1%), whereas 16.8% of the samples belonged to other SARS-CoV-2 (sub)lineages. The detected SARS-CoV-2 (sub)lineages resulted in eight COVID-19 pandemic waves in Serbia, which correspond to the pandemic waves reported in Europe and the United States. Wave dynamics in Serbia showed the most resemblance with the profile of pandemic waves in southern Europe, consistent with the southeastern European location of Serbia. The samples were assigned to sixteen SARS-CoV-2 Nextstrain clades: 20A, 20B, 20C, 20D, 20E, 20G, 20I, 21J, 21K, 21L, 22A, 22B, 22C, 22D, 22E, and 22F and six different Omicron recombinants (XZ, XAZ, XAS, XBB, XBF, and XBK). The 10 most common mutations detected in the coding and untranslated regions of the SARS-CoV-2 genomes included four mutations affecting the spike protein (S:D614G, S:T478K, S:P681H, and S:S477N) and one mutation at each of the following positions: 5′-untranslated region (5’UTR:241); N protein (N:RG203KR); NSP3 protein (NSP3:F106F); NSP4 protein (NSP4:T492I); NSP6 protein (NSP6: S106/G107/F108 - triple deletion), and NSP12b protein (NSP12b:P314L). This national-level study is the most comprehensive in terms of sequencing and genomic surveillance of SARS-CoV-2 during the pandemic in Serbia, highlighting the importance of establishing and maintaining good national practice for monitoring SARS-CoV-2 and other viruses circulating worldwide.",
publisher = "Frontiers",
journal = "Frontiers in Microbiology, Frontiers in Microbiology",
title = "Genome sequence diversity of SARS-CoV-2 in Serbia: insights gained from a 3-year pandemic study",
volume = "15",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2327"
}

Novković, M., Banović Đeri, B., RistivojeviĆ, B., Knežević, A., Janković, M., Tanasić, V., Radojičić, V., Keckarević, D., Vidanović, D., Tešović, B., Skakić, A., Tolinački, M., Morić, I.,& Đorđević, V.. (2024). Genome sequence diversity of SARS-CoV-2 in Serbia: insights gained from a 3-year pandemic study. in Frontiers in Microbiology
Frontiers., 15.
https://hdl.handle.net/21.15107/rcub_imagine_2327

Novković M, Banović Đeri B, RistivojeviĆ B, Knežević A, Janković M, Tanasić V, Radojičić V, Keckarević D, Vidanović D, Tešović B, Skakić A, Tolinački M, Morić I, Đorđević V. Genome sequence diversity of SARS-CoV-2 in Serbia: insights gained from a 3-year pandemic study. in Frontiers in Microbiology. 2024;15.
https://hdl.handle.net/21.15107/rcub_imagine_2327 .

Novković, Mirjana, Banović Đeri, Bojana, RistivojeviĆ, Bojan, Knežević, Aleksandra, Janković, Marko, Tanasić, Vanja, Radojičić, Verica, Keckarević, Dusan, Vidanović, Dejan, Tešović, Bojana, Skakić, Anita, Tolinački, Maja, Morić, Ivana, Đorđević, Valentina, "Genome sequence diversity of SARS-CoV-2 in Serbia: insights gained from a 3-year pandemic study" in Frontiers in Microbiology, 15 (2024),
https://hdl.handle.net/21.15107/rcub_imagine_2327 .

TY  - CONF
AU  - Nikolić, Dragana
AU  - Divac Rankov, Aleksandra
AU  - Samardžić, Jelena
AU  - Pantelić, Ana
AU  - Spasovski, Vesna
AU  - Banović Đeri, Bojana
AU  - Kosanović, Maja
PY  - 2023
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2266
AB  - Outer membrane vesicles (OMVs), extracellular vesicles (EVs) produced by Gram-negative bacteria, are
increasingly recognised as promising tools in biomedicine due to their innate ability to interact with human
cells and trigger immune responses. The interaction of OMVs of plant growth-promoting bacteria (PGPB) with
plants, as well as with plant-pathogenic microorganisms, is far less explored. Considering the great
importance of PGPBs for the development of sustainable, environmentally friendly solutions in agriculture, the
study of the role of OMVs in PGPB-plant and PGPB-phytopathogen interactions holds valuable application
potential.
To investigate PGPB OMVs, we isolated and characterised OMVs produced by Paraburkholderia phytofirmans
PsJN, a PGPB strain known to enhance plant resistance to various abiotic and biotic stresses. After testing
different methods for isolating and purifying OMVs, a commercially available affinity-based column system
was selected as the most efficient. Outer membrane origin of isolated OMVs was confirmed using an essay for
detection of lipopolysaccharide (LPS).
To examine the interaction of OMVs with plant cells, Arabidopsis thaliana roots were incubated with isolated
P. phytofirmans PsJN vesicles, previously labelled with lipid binding fluorescent dye Vybrant™ DiD. Red signals
were observed, under confocal laser scanning microscope, in root hairs and root surface in DiD-OMV treated
plants, while in control-treated roots the same signals were missing. The results suggest direct contact of
OMVs with root hairs, which are necessary for nutrient acquisition and plant-microbe interactions in
rhizosphere. Our further research is focused on the characterization of OMV-associated RNA and its potential
delivery into host plant cells.
PB  - Serbian Society for Extracellular Vesicles (SrbEVs)
PB  - Austrian Society for Extracellular Vesicles (ASEV)
PB  - Hungarian Society for Extracellular Vesicles (HSEV)
PB  - Slovenian Network for Extracellular Vesicles (SiN-EV)
C3  - Small New World 2.0
T1  - Exploring the interaction of Outer membrane vesicles (OMVs) produced by Paraburkholderia phytofirmans PsJN with Arabidopsis thaliana roots
EP  - 109
SP  - 109
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2266
ER  - 

@conference{
author = "Nikolić, Dragana and Divac Rankov, Aleksandra and Samardžić, Jelena and Pantelić, Ana and Spasovski, Vesna and Banović Đeri, Bojana and Kosanović, Maja",
year = "2023",
abstract = "Outer membrane vesicles (OMVs), extracellular vesicles (EVs) produced by Gram-negative bacteria, are
increasingly recognised as promising tools in biomedicine due to their innate ability to interact with human
cells and trigger immune responses. The interaction of OMVs of plant growth-promoting bacteria (PGPB) with
plants, as well as with plant-pathogenic microorganisms, is far less explored. Considering the great
importance of PGPBs for the development of sustainable, environmentally friendly solutions in agriculture, the
study of the role of OMVs in PGPB-plant and PGPB-phytopathogen interactions holds valuable application
potential.
To investigate PGPB OMVs, we isolated and characterised OMVs produced by Paraburkholderia phytofirmans
PsJN, a PGPB strain known to enhance plant resistance to various abiotic and biotic stresses. After testing
different methods for isolating and purifying OMVs, a commercially available affinity-based column system
was selected as the most efficient. Outer membrane origin of isolated OMVs was confirmed using an essay for
detection of lipopolysaccharide (LPS).
To examine the interaction of OMVs with plant cells, Arabidopsis thaliana roots were incubated with isolated
P. phytofirmans PsJN vesicles, previously labelled with lipid binding fluorescent dye Vybrant™ DiD. Red signals
were observed, under confocal laser scanning microscope, in root hairs and root surface in DiD-OMV treated
plants, while in control-treated roots the same signals were missing. The results suggest direct contact of
OMVs with root hairs, which are necessary for nutrient acquisition and plant-microbe interactions in
rhizosphere. Our further research is focused on the characterization of OMV-associated RNA and its potential
delivery into host plant cells.",
publisher = "Serbian Society for Extracellular Vesicles (SrbEVs), Austrian Society for Extracellular Vesicles (ASEV), Hungarian Society for Extracellular Vesicles (HSEV), Slovenian Network for Extracellular Vesicles (SiN-EV)",
journal = "Small New World 2.0",
title = "Exploring the interaction of Outer membrane vesicles (OMVs) produced by Paraburkholderia phytofirmans PsJN with Arabidopsis thaliana roots",
pages = "109-109",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2266"
}

Nikolić, D., Divac Rankov, A., Samardžić, J., Pantelić, A., Spasovski, V., Banović Đeri, B.,& Kosanović, M.. (2023). Exploring the interaction of Outer membrane vesicles (OMVs) produced by Paraburkholderia phytofirmans PsJN with Arabidopsis thaliana roots. in Small New World 2.0
Serbian Society for Extracellular Vesicles (SrbEVs)., 109-109.
https://hdl.handle.net/21.15107/rcub_imagine_2266

Nikolić D, Divac Rankov A, Samardžić J, Pantelić A, Spasovski V, Banović Đeri B, Kosanović M. Exploring the interaction of Outer membrane vesicles (OMVs) produced by Paraburkholderia phytofirmans PsJN with Arabidopsis thaliana roots. in Small New World 2.0. 2023;:109-109.
https://hdl.handle.net/21.15107/rcub_imagine_2266 .

Nikolić, Dragana, Divac Rankov, Aleksandra, Samardžić, Jelena, Pantelić, Ana, Spasovski, Vesna, Banović Đeri, Bojana, Kosanović, Maja, "Exploring the interaction of Outer membrane vesicles (OMVs) produced by Paraburkholderia phytofirmans PsJN with Arabidopsis thaliana roots" in Small New World 2.0 (2023):109-109,
https://hdl.handle.net/21.15107/rcub_imagine_2266 .

TY  - JOUR
AU  - Marić, Slađana
AU  - Radičević, Sanja
AU  - Milošević, Nebojša
AU  - Glišić, Ivana
AU  - Đorđević, Milena
AU  - Banović Đeri, Bojana
PY  - 2023
UR  - http://doi.fil.bg.ac.rs/volume.php?pt=journals&issue=pomology-2023-57-217_218&i=2
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2278
AB  - Identification of the S-genotypes in landraces is a crucial step in the molecular characteri- zation of Serbian autochthonous sweet cherry germplasm. It is also of enormous significance for bre- eders and growers, as this fruit species exhibits a gametophytic self-incompatibility, controlled by the  multi-allelic two genes of the S-locus. The aim of this study was to summarize known information  and reveal new data on the S-alleles in 23 sweet cherry landraces originating in the Republic of Ser- bia. The use of polymerase chain reaction (PCR) with consensus primers for the second intron of S- RNase, primers specific for S-RNase and certain SFB alleles, along with DNA fragment analysis  using fluorescently labelled forward primers to amplify both the S-RNase first intron and the SFB in- tron, revealed 10 alleles (S1 to S6, S9, S12, S13 and S22) that generated the following 13 S-genotypes:  S1S2 (one landrace), S1S4 (one landrace), S1S5 (one landrace), S2S3 (four landraces), S3S4 (two lan- draces), S3S5 (two landraces), S3S6 (three landraces), S3S9 (two landraces), S3S12 (two landraces),  S4S5 (one landrace), S4S13 (one landrace), S5S22 (one landrace) and S6S9 (two landraces). The most  frequent S-allele and S-genotype in this sweet cherry material were S3 and S2S3, with occurrence fre- quencies of 32.6% and 17.4%, respectively. Based on the obtained results, the sweet cherry landraces  were assigned to 12 incompatibility groups and one group of universal donors (‘0’). These results pro- vide important information about their cross-compatibility and the diversity of the S-locus in Serbian  sweet cherry germplasm.
T2  - Voćarstvo
T1  - An Overview of S-Genotype Diversity in Sweet Cherry Landraces Grown in the Central Region of the Republic of Serbia
EP  - 103
IS  - 217-218
SP  - 93
VL  - 57
DO  - 10.18485/pomology.2023.57.217_218.2
ER  - 

@article{
author = "Marić, Slađana and Radičević, Sanja and Milošević, Nebojša and Glišić, Ivana and Đorđević, Milena and Banović Đeri, Bojana",
year = "2023",
abstract = "Identification of the S-genotypes in landraces is a crucial step in the molecular characteri- zation of Serbian autochthonous sweet cherry germplasm. It is also of enormous significance for bre- eders and growers, as this fruit species exhibits a gametophytic self-incompatibility, controlled by the  multi-allelic two genes of the S-locus. The aim of this study was to summarize known information  and reveal new data on the S-alleles in 23 sweet cherry landraces originating in the Republic of Ser- bia. The use of polymerase chain reaction (PCR) with consensus primers for the second intron of S- RNase, primers specific for S-RNase and certain SFB alleles, along with DNA fragment analysis  using fluorescently labelled forward primers to amplify both the S-RNase first intron and the SFB in- tron, revealed 10 alleles (S1 to S6, S9, S12, S13 and S22) that generated the following 13 S-genotypes:  S1S2 (one landrace), S1S4 (one landrace), S1S5 (one landrace), S2S3 (four landraces), S3S4 (two lan- draces), S3S5 (two landraces), S3S6 (three landraces), S3S9 (two landraces), S3S12 (two landraces),  S4S5 (one landrace), S4S13 (one landrace), S5S22 (one landrace) and S6S9 (two landraces). The most  frequent S-allele and S-genotype in this sweet cherry material were S3 and S2S3, with occurrence fre- quencies of 32.6% and 17.4%, respectively. Based on the obtained results, the sweet cherry landraces  were assigned to 12 incompatibility groups and one group of universal donors (‘0’). These results pro- vide important information about their cross-compatibility and the diversity of the S-locus in Serbian  sweet cherry germplasm.",
journal = "Voćarstvo",
title = "An Overview of S-Genotype Diversity in Sweet Cherry Landraces Grown in the Central Region of the Republic of Serbia",
pages = "103-93",
number = "217-218",
volume = "57",
doi = "10.18485/pomology.2023.57.217_218.2"
}

Marić, S., Radičević, S., Milošević, N., Glišić, I., Đorđević, M.,& Banović Đeri, B.. (2023). An Overview of S-Genotype Diversity in Sweet Cherry Landraces Grown in the Central Region of the Republic of Serbia. in Voćarstvo, 57(217-218), 93-103.
https://doi.org/10.18485/pomology.2023.57.217_218.2

Marić S, Radičević S, Milošević N, Glišić I, Đorđević M, Banović Đeri B. An Overview of S-Genotype Diversity in Sweet Cherry Landraces Grown in the Central Region of the Republic of Serbia. in Voćarstvo. 2023;57(217-218):93-103.
doi:10.18485/pomology.2023.57.217_218.2 .

Marić, Slađana, Radičević, Sanja, Milošević, Nebojša, Glišić, Ivana, Đorđević, Milena, Banović Đeri, Bojana, "An Overview of S-Genotype Diversity in Sweet Cherry Landraces Grown in the Central Region of the Republic of Serbia" in Voćarstvo, 57, no. 217-218 (2023):93-103,
https://doi.org/10.18485/pomology.2023.57.217_218.2 . .

TY  - CONF
AU  - Božić, Manja
AU  - Ignjatović-Micić, Dragana
AU  - Delić, Nenad
AU  - Mladenović, Marko
AU  - Vančetović, Jelena
AU  - Banović Đeri, Bojana
AU  - Nikolić, Ana
PY  - 2023
UR  - https://belbi.bg.ac.rs/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2007
AB  - Micro RNAs (miRNAs) are known regulators of various processes in plants, including growth,
development and stress responses. They achieve this through mRNA cleavage or translational
inhibition, in a process called RNA interference. Herein, their role in chilling stress response in
young maize seedlings (Zea mays L.) is examined, using high-throughput sequencing methods.
Bringing light to all aspects of chilling stress response in maize is necessary since earlier
sowing, during colder periods, is one of the most promising strategies of avoiding maize yield
loss due to effects of climate change in these areas.
Sterilized seeds of two maize genotypes (tolerant - T and sensitive - S to low temperatures)
were germinated in the dark for five days (optimal conditions), after which the 5-d old seedlings
were exposed to chilling conditions for 6h (10° C). Samples for RNA isolation and cDNA library
preparation were taken after the treatment ended, and single-end 50 bp sequencing was
performed (Illumina® Novaseq 6000). The miRNAs were then filtered, mapped, identified
and quantified using adequate bioinformatics tools; and the differential expression analysis
was carried out using the DEGseq R package. The analysis was performed on 859 miRNAs,
after previously executed TPM normalization using the MA-plot-based method with random
sampling model (MARS). The threshold for significantly differential expression was set as the
Bayesian adjusted p-value, or q-value < 0.01 and log2 fold change > 1.
A total of 612 were expressed differentially, but only 55 miRNAs were common for both
genotypes and at the same time differentially expressed between control and treatment
conditions – 40 novel and 15 known. Half of the common miRNAs showed the same
expression patterns in both genotypes, while the other half did not. Among them, seven known
miRNAs showed opposing expression patterns between the genotypes (zma-miR167b-3p
zma-miR167e-3p, zma-miR159c-5p, zma-miR164g-3p, zma-miR166a-5p, zma-miR398a-
3p, and zma-miR528a-3p). These miRNAs were shown to have a role in various abiotic stress
responses, including drought, waterlogging, high salts – but not chilling. While the results point
to their potential role in establishing chilling tolerance in maize seedlings, further research is
necessary to confirm it and connect the miRNAs to their potential targets.
PB  - Belgrade : Institute of molecular genetics and genetic engineering
C3  - 4th Belgrade Bioinformatics Conference
T1  - Seven miRNAs potentially included in the chilling response of maize plants in early stages of development
EP  - 83
SP  - 83
VL  - 4
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2007
ER  - 

@conference{
author = "Božić, Manja and Ignjatović-Micić, Dragana and Delić, Nenad and Mladenović, Marko and Vančetović, Jelena and Banović Đeri, Bojana and Nikolić, Ana",
year = "2023",
abstract = "Micro RNAs (miRNAs) are known regulators of various processes in plants, including growth,
development and stress responses. They achieve this through mRNA cleavage or translational
inhibition, in a process called RNA interference. Herein, their role in chilling stress response in
young maize seedlings (Zea mays L.) is examined, using high-throughput sequencing methods.
Bringing light to all aspects of chilling stress response in maize is necessary since earlier
sowing, during colder periods, is one of the most promising strategies of avoiding maize yield
loss due to effects of climate change in these areas.
Sterilized seeds of two maize genotypes (tolerant - T and sensitive - S to low temperatures)
were germinated in the dark for five days (optimal conditions), after which the 5-d old seedlings
were exposed to chilling conditions for 6h (10° C). Samples for RNA isolation and cDNA library
preparation were taken after the treatment ended, and single-end 50 bp sequencing was
performed (Illumina® Novaseq 6000). The miRNAs were then filtered, mapped, identified
and quantified using adequate bioinformatics tools; and the differential expression analysis
was carried out using the DEGseq R package. The analysis was performed on 859 miRNAs,
after previously executed TPM normalization using the MA-plot-based method with random
sampling model (MARS). The threshold for significantly differential expression was set as the
Bayesian adjusted p-value, or q-value < 0.01 and log2 fold change > 1.
A total of 612 were expressed differentially, but only 55 miRNAs were common for both
genotypes and at the same time differentially expressed between control and treatment
conditions – 40 novel and 15 known. Half of the common miRNAs showed the same
expression patterns in both genotypes, while the other half did not. Among them, seven known
miRNAs showed opposing expression patterns between the genotypes (zma-miR167b-3p
zma-miR167e-3p, zma-miR159c-5p, zma-miR164g-3p, zma-miR166a-5p, zma-miR398a-
3p, and zma-miR528a-3p). These miRNAs were shown to have a role in various abiotic stress
responses, including drought, waterlogging, high salts – but not chilling. While the results point
to their potential role in establishing chilling tolerance in maize seedlings, further research is
necessary to confirm it and connect the miRNAs to their potential targets.",
publisher = "Belgrade : Institute of molecular genetics and genetic engineering",
journal = "4th Belgrade Bioinformatics Conference",
title = "Seven miRNAs potentially included in the chilling response of maize plants in early stages of development",
pages = "83-83",
volume = "4",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2007"
}

Božić, M., Ignjatović-Micić, D., Delić, N., Mladenović, M., Vančetović, J., Banović Đeri, B.,& Nikolić, A.. (2023). Seven miRNAs potentially included in the chilling response of maize plants in early stages of development. in 4th Belgrade Bioinformatics Conference
Belgrade : Institute of molecular genetics and genetic engineering., 4, 83-83.
https://hdl.handle.net/21.15107/rcub_imagine_2007

Božić M, Ignjatović-Micić D, Delić N, Mladenović M, Vančetović J, Banović Đeri B, Nikolić A. Seven miRNAs potentially included in the chilling response of maize plants in early stages of development. in 4th Belgrade Bioinformatics Conference. 2023;4:83-83.
https://hdl.handle.net/21.15107/rcub_imagine_2007 .

Božić, Manja, Ignjatović-Micić, Dragana, Delić, Nenad, Mladenović, Marko, Vančetović, Jelena, Banović Đeri, Bojana, Nikolić, Ana, "Seven miRNAs potentially included in the chilling response of maize plants in early stages of development" in 4th Belgrade Bioinformatics Conference, 4 (2023):83-83,
https://hdl.handle.net/21.15107/rcub_imagine_2007 .

TY  - CONF
AU  - Milić, Dejana
AU  - Pantelić, Ana
AU  - Samardžić, Jelena
AU  - Banović Đeri, Bojana
AU  - Vidović, Marija
PY  - 2023
UR  - https://belbi.bg.ac.rs/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2035
AB  - Variegated Pelargonium zonale is a widely cultivated ornamental plant characterized by
green, photosynthetically active tissue (GL) and white, non-photosynthetic tissue (WL).
The aim of this study was to investigate the transcriptomic differences between these
two tissue types.
We performed RNA-seq analysis of GL and WL on Illumina HiSeq 2500 platform. The
raw reads were processed using in-house scripts to remove low-quality reads, adapter
sequences, poly-N sequences, and contaminants. High-quality clean reads were subjected
to de novo transcriptome assembly using Trinity (min_kmer_cov = 2, min_glue = 2). The
redundancy was removed and longest transcripts per cluster were selected as unigenes.
Gene expression levels were estimated using RSEM by mapping clean data back to the
assembled transcriptome (Bowtie2 with mismatch = 0). Differential expression analysis
between GL and WL (three biological replicates per each) was performed with DESeq2
R package (p values adjusted according to Benjamini and Hochberg for controlling False
Discovery Rate). Genes with abs (log2 FC) ≥ 2 and adjusted p value < 0.05 were assigned
as statistically significant differentially expressed. Functional enrichment analysis was
performed using GOseq R package and KOBAS software (corrected p < 0.05).
We annotated 85,374 unigenes (61.17%), providing a valuable resource for future
functional genomics studies. Out of 8896 gene clusters that were statistically significantly
differentially expressed between the green and white leaf tissues (p value < 0.05 and
abs(log2 fold change) ≥ 2), 5585 were upregulated in the WL, while 3311 were upregulated
in the GL. These findings shed light on the transcriptomic differences between the
two leaf tissue types in P. zonale and provide a foundation for further research on the
functional significance of these differences. Also, this study demonstrated utility of the
Trinity pipeline for de novo transcriptomic analysis of organism whose genomes are yet
not sequenced.
PB  - Belgrade : Institute of molecular genetics and genetic engineering
C3  - 4th Belgrade Bioinformatics Conference
T1  - Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale
EP  - 90
SP  - 90
VL  - 4
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2035
ER  - 

@conference{
author = "Milić, Dejana and Pantelić, Ana and Samardžić, Jelena and Banović Đeri, Bojana and Vidović, Marija",
year = "2023",
abstract = "Variegated Pelargonium zonale is a widely cultivated ornamental plant characterized by
green, photosynthetically active tissue (GL) and white, non-photosynthetic tissue (WL).
The aim of this study was to investigate the transcriptomic differences between these
two tissue types.
We performed RNA-seq analysis of GL and WL on Illumina HiSeq 2500 platform. The
raw reads were processed using in-house scripts to remove low-quality reads, adapter
sequences, poly-N sequences, and contaminants. High-quality clean reads were subjected
to de novo transcriptome assembly using Trinity (min_kmer_cov = 2, min_glue = 2). The
redundancy was removed and longest transcripts per cluster were selected as unigenes.
Gene expression levels were estimated using RSEM by mapping clean data back to the
assembled transcriptome (Bowtie2 with mismatch = 0). Differential expression analysis
between GL and WL (three biological replicates per each) was performed with DESeq2
R package (p values adjusted according to Benjamini and Hochberg for controlling False
Discovery Rate). Genes with abs (log2 FC) ≥ 2 and adjusted p value < 0.05 were assigned
as statistically significant differentially expressed. Functional enrichment analysis was
performed using GOseq R package and KOBAS software (corrected p < 0.05).
We annotated 85,374 unigenes (61.17%), providing a valuable resource for future
functional genomics studies. Out of 8896 gene clusters that were statistically significantly
differentially expressed between the green and white leaf tissues (p value < 0.05 and
abs(log2 fold change) ≥ 2), 5585 were upregulated in the WL, while 3311 were upregulated
in the GL. These findings shed light on the transcriptomic differences between the
two leaf tissue types in P. zonale and provide a foundation for further research on the
functional significance of these differences. Also, this study demonstrated utility of the
Trinity pipeline for de novo transcriptomic analysis of organism whose genomes are yet
not sequenced.",
publisher = "Belgrade : Institute of molecular genetics and genetic engineering",
journal = "4th Belgrade Bioinformatics Conference",
title = "Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale",
pages = "90-90",
volume = "4",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2035"
}

Milić, D., Pantelić, A., Samardžić, J., Banović Đeri, B.,& Vidović, M.. (2023). Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale. in 4th Belgrade Bioinformatics Conference
Belgrade : Institute of molecular genetics and genetic engineering., 4, 90-90.
https://hdl.handle.net/21.15107/rcub_imagine_2035

Milić D, Pantelić A, Samardžić J, Banović Đeri B, Vidović M. Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale. in 4th Belgrade Bioinformatics Conference. 2023;4:90-90.
https://hdl.handle.net/21.15107/rcub_imagine_2035 .

Milić, Dejana, Pantelić, Ana, Samardžić, Jelena, Banović Đeri, Bojana, Vidović, Marija, "Efficient bioinformatics workflow for de novo transcriptome assembly of Pelargonium zonale" in 4th Belgrade Bioinformatics Conference, 4 (2023):90-90,
https://hdl.handle.net/21.15107/rcub_imagine_2035 .

TY  - CONF
AU  - Novković, Mirjana
AU  - Banović Đeri, Bojana
AU  - Todorović, Saša
AU  - Đorđević, Valentina
PY  - 2023
UR  - https://belbi.bg.ac.rs/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2021
AB  - The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global
pandemic, resulting in significant morbidity and mortality worldwide. Understanding the evolutionary
dynamics and genetic diversity of the virus were crucial for virus control and management
strategies. With that aim we conducted genomic surveillance and phylogenetic analysis of
SARS-CoV-2 variants in Serbia, spanning from March 2020 to the end of January 2023.
Sequencing was conducted using three different platforms: Oxford Nanopore, Ion Torrent AmpliSeq
and BGISEQ-500. Consensus sequences obtained using platforms respective software were deposited
in the GISAID database. In this study 2109 good-quality sequences were included (doi.10.55876/
gis8.230411qh). Pangolin and Nextclade software were utilized for clade, lineage and variant
determination, while sequence alignment and construction of the phylogenetic tree was performed
using Nextstrain web-based application.
Variant analysis revealed over 125,000 mutations across the 2109 sequences, of which 38% occurred in
the S protein encoding gene. The most common mutations involved intragenic single nucleotide variants
(88%), followed by intragenic deletions (5%). All sequences were assigned to following 16 clades: 20A,
20B, 20C, 20D, 20E, 20G, 20I, 21J, 21K, 21L, 22A, 22B, 22C, 22D, 22E, and 22F.
Temporal analysis of the variants in Serbia revealed that the Alpha variant was predominant during 2020
and the first three months of 2021. The Delta variant emerged in June 2021, dominating until the end
of December 2021, when Omicron variant was detected for the first time, overtaking the dominance for
the remaining surveillance period. Notably, the Gamma and Epsilon variants were not detected in the
analyzed samples.
Phylogenetic analysis demonstrated that the SARS-CoV-2 variants circulating in Serbia were largely
comparable to the variants found in Europe. However, a slight delay in their emergence was observed,
potentially attributed to a lower travel rate during that period and a decreased frequency of sequencing
in certain months.
PB  - Belgrade : Institute of molecular genetics and genetic engineering
C3  - 4th Belgrade Bioinformatics Conference
T1  - Genomic Surveillance and Phylogenetic Analysis of SARS-CoV-2 Variants in Serbia: Insights into Evolutionary Dynamics and Genetic Diversity
EP  - 81
SP  - 81
VL  - 4
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2021
ER  - 

@conference{
author = "Novković, Mirjana and Banović Đeri, Bojana and Todorović, Saša and Đorđević, Valentina",
year = "2023",
abstract = "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global
pandemic, resulting in significant morbidity and mortality worldwide. Understanding the evolutionary
dynamics and genetic diversity of the virus were crucial for virus control and management
strategies. With that aim we conducted genomic surveillance and phylogenetic analysis of
SARS-CoV-2 variants in Serbia, spanning from March 2020 to the end of January 2023.
Sequencing was conducted using three different platforms: Oxford Nanopore, Ion Torrent AmpliSeq
and BGISEQ-500. Consensus sequences obtained using platforms respective software were deposited
in the GISAID database. In this study 2109 good-quality sequences were included (doi.10.55876/
gis8.230411qh). Pangolin and Nextclade software were utilized for clade, lineage and variant
determination, while sequence alignment and construction of the phylogenetic tree was performed
using Nextstrain web-based application.
Variant analysis revealed over 125,000 mutations across the 2109 sequences, of which 38% occurred in
the S protein encoding gene. The most common mutations involved intragenic single nucleotide variants
(88%), followed by intragenic deletions (5%). All sequences were assigned to following 16 clades: 20A,
20B, 20C, 20D, 20E, 20G, 20I, 21J, 21K, 21L, 22A, 22B, 22C, 22D, 22E, and 22F.
Temporal analysis of the variants in Serbia revealed that the Alpha variant was predominant during 2020
and the first three months of 2021. The Delta variant emerged in June 2021, dominating until the end
of December 2021, when Omicron variant was detected for the first time, overtaking the dominance for
the remaining surveillance period. Notably, the Gamma and Epsilon variants were not detected in the
analyzed samples.
Phylogenetic analysis demonstrated that the SARS-CoV-2 variants circulating in Serbia were largely
comparable to the variants found in Europe. However, a slight delay in their emergence was observed,
potentially attributed to a lower travel rate during that period and a decreased frequency of sequencing
in certain months.",
publisher = "Belgrade : Institute of molecular genetics and genetic engineering",
journal = "4th Belgrade Bioinformatics Conference",
title = "Genomic Surveillance and Phylogenetic Analysis of SARS-CoV-2 Variants in Serbia: Insights into Evolutionary Dynamics and Genetic Diversity",
pages = "81-81",
volume = "4",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2021"
}

Novković, M., Banović Đeri, B., Todorović, S.,& Đorđević, V.. (2023). Genomic Surveillance and Phylogenetic Analysis of SARS-CoV-2 Variants in Serbia: Insights into Evolutionary Dynamics and Genetic Diversity. in 4th Belgrade Bioinformatics Conference
Belgrade : Institute of molecular genetics and genetic engineering., 4, 81-81.
https://hdl.handle.net/21.15107/rcub_imagine_2021

Novković M, Banović Đeri B, Todorović S, Đorđević V. Genomic Surveillance and Phylogenetic Analysis of SARS-CoV-2 Variants in Serbia: Insights into Evolutionary Dynamics and Genetic Diversity. in 4th Belgrade Bioinformatics Conference. 2023;4:81-81.
https://hdl.handle.net/21.15107/rcub_imagine_2021 .

Novković, Mirjana, Banović Đeri, Bojana, Todorović, Saša, Đorđević, Valentina, "Genomic Surveillance and Phylogenetic Analysis of SARS-CoV-2 Variants in Serbia: Insights into Evolutionary Dynamics and Genetic Diversity" in 4th Belgrade Bioinformatics Conference, 4 (2023):81-81,
https://hdl.handle.net/21.15107/rcub_imagine_2021 .

TY  - JOUR
AU  - Milić, Dejana
AU  - Pantelić, Ana
AU  - Banović Đeri, Bojana
AU  - Samardžić, Jelena
AU  - Vidović, Marija
PY  - 2023
UR  - https://www.mdpi.com/1422-0067/24/6/5288
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1795
AB  - The photosynthetically active green leaf (GL) and non-active white leaf (WL) tissues of variegated Pelargonium zonale provide an excellent model system for studying processes associated with photosynthesis and sink-source interactions, enabling the same microenvironmental conditions. By combining differential transcriptomics and metabolomics, we identified the main differences between these two metabolically contrasting tissues. Genes related to photosynthesis and associated pigments, the Calvin–Benson cycle, fermentation, and glycolysis were strongly repressed in WL. On the other hand, genes related to nitrogen and protein metabolism, defence, cytoskeletal components (motor proteins), cell division, DNA replication, repair and recombination, chromatin remodelling, and histone modifications were upregulated in WL. A content of soluble sugars, TCA intermediates, ascorbate, and hydroxybenzoic acids was lower, while the concentration of free amino acids (AAs), hydroxycinnamic acids, and several quercetin and kaempferol glycosides was higher in WL than in GL. Therefore, WL presents a carbon sink and depends on photosynthetic and energy-generating processes in GL. Furthermore, the upregulated nitrogen metabolism in WL compensates for the insufficient energy from carbon metabolism by providing alternative respiratory substrates. At the same time, WL serves as nitrogen storage. Overall, our study provides a new genetic data resource for the use of this excellent model system and for ornamental pelargonium breeding and contributes to uncovering molecular mechanisms underlying variegation and its adaptive ecological value.
T2  - International Journal of Molecular Sciences
T2  - International Journal of Molecular Sciences
T1  - Contrasting Metabolisms in Green and White Leaf Sectors of Variegated Pelargonium zonale—An Integrative Transcriptomic and Metabolomic Study
IS  - 6
SP  - 5288
VL  - 24
DO  - 10.3390/ijms24065288
ER  - 

@article{
author = "Milić, Dejana and Pantelić, Ana and Banović Đeri, Bojana and Samardžić, Jelena and Vidović, Marija",
year = "2023",
abstract = "The photosynthetically active green leaf (GL) and non-active white leaf (WL) tissues of variegated Pelargonium zonale provide an excellent model system for studying processes associated with photosynthesis and sink-source interactions, enabling the same microenvironmental conditions. By combining differential transcriptomics and metabolomics, we identified the main differences between these two metabolically contrasting tissues. Genes related to photosynthesis and associated pigments, the Calvin–Benson cycle, fermentation, and glycolysis were strongly repressed in WL. On the other hand, genes related to nitrogen and protein metabolism, defence, cytoskeletal components (motor proteins), cell division, DNA replication, repair and recombination, chromatin remodelling, and histone modifications were upregulated in WL. A content of soluble sugars, TCA intermediates, ascorbate, and hydroxybenzoic acids was lower, while the concentration of free amino acids (AAs), hydroxycinnamic acids, and several quercetin and kaempferol glycosides was higher in WL than in GL. Therefore, WL presents a carbon sink and depends on photosynthetic and energy-generating processes in GL. Furthermore, the upregulated nitrogen metabolism in WL compensates for the insufficient energy from carbon metabolism by providing alternative respiratory substrates. At the same time, WL serves as nitrogen storage. Overall, our study provides a new genetic data resource for the use of this excellent model system and for ornamental pelargonium breeding and contributes to uncovering molecular mechanisms underlying variegation and its adaptive ecological value.",
journal = "International Journal of Molecular Sciences, International Journal of Molecular Sciences",
title = "Contrasting Metabolisms in Green and White Leaf Sectors of Variegated Pelargonium zonale—An Integrative Transcriptomic and Metabolomic Study",
number = "6",
pages = "5288",
volume = "24",
doi = "10.3390/ijms24065288"
}

Milić, D., Pantelić, A., Banović Đeri, B., Samardžić, J.,& Vidović, M.. (2023). Contrasting Metabolisms in Green and White Leaf Sectors of Variegated Pelargonium zonale—An Integrative Transcriptomic and Metabolomic Study. in International Journal of Molecular Sciences, 24(6), 5288.
https://doi.org/10.3390/ijms24065288

Milić D, Pantelić A, Banović Đeri B, Samardžić J, Vidović M. Contrasting Metabolisms in Green and White Leaf Sectors of Variegated Pelargonium zonale—An Integrative Transcriptomic and Metabolomic Study. in International Journal of Molecular Sciences. 2023;24(6):5288.
doi:10.3390/ijms24065288 .

Milić, Dejana, Pantelić, Ana, Banović Đeri, Bojana, Samardžić, Jelena, Vidović, Marija, "Contrasting Metabolisms in Green and White Leaf Sectors of Variegated Pelargonium zonale—An Integrative Transcriptomic and Metabolomic Study" in International Journal of Molecular Sciences, 24, no. 6 (2023):5288,
https://doi.org/10.3390/ijms24065288 . .

TY  - CONF
AU  - Banović Đeri, Bojana
AU  - Nešić, Sofija
AU  - Pantelić, Ana
AU  - Samardžić, Jelena
AU  - Nikolić, Dragana
PY  - 2023
UR  - https://belbi.bg.ac.rs/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2030
AB  - Bacterial small RNAs (sRNAs) represent a highly diverse RNA class ranging from 8 to 200
nucleotides in length, originating from the bacterial chromosome, plasmids or phages.
After syntheses sRNAs can remain inside the bacterial cell, be secreted or packed into
outer membrane vesicles (OMV), enabling various intra- and inter-kingdom interactions.
Different sRNAs biotypes display differences in structure, mechanism of action and level
of regulation (i.e. transcription, translation, mRNA stability, etc.), but could be broadly
grouped in: trans-acting sRNAs (bind to target mRNAs) and cis-encoded sRNAs (or
antisense RNA that may interact not only with mRNAs, but also with proteins and DNA).
Even though the advancement of high-throughput sequencing technology led to a burst
of knowledge on small RNAs complexity and diversity, there are still specific challenges
related to sRNA-seq data analysis that need to be resolved. Two main challenges,
associated to short length of many bacterial sRNA biotypes, are: (i) to discriminate
between functional sRNAs synthesized by bacterial cell and degradation fragments
produced by sample preparation and (ii) to detect functional sRNAs displaying sequence
variation. While loss of very small sized sRNAs could easily be overcome by cutting-off
only the specific adapter sequences that were used in sRNA library preparation, providing
a proper mapping still remains a strenuous task.
The aim of this study was to test five different mapping tools that are widely used in NGS
data analysis (bbmap, bowtie2, bwa, minimap2 and segemehl) for their performances in
mapping of bacterial OMV sRNA-seq data to bacterial reference genome. For this test
publicly available NCBI sRNA-seq dataset from OMVs of Aliivibrio fischeri (PRJNA629425)
was used, as it contained sRNAs of different length and biotype and because A.fischeri
reference genome and annotation were available (PRJNA12986). We evaluated five
mappers using alignment and assignment rates as well as computational time. Alignment
rate was calculated as the ratio of aligned and input reads, while the assignment rate
was calculated as the ratio of assigned and aligned reads. Finally, totals of detected
sRNAs biotypes were compared between different mappers. The statistical analysis was
performed in R (version 4.3.0) and performance metrics are discussed.
PB  - Belgrade : Institute of molecular genetics and genetic engineering
C3  - 4th Belgrade Bioinformatics Conference
T1  - Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles
EP  - 85
SP  - 85
VL  - 4
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2030
ER  - 

@conference{
author = "Banović Đeri, Bojana and Nešić, Sofija and Pantelić, Ana and Samardžić, Jelena and Nikolić, Dragana",
year = "2023",
abstract = "Bacterial small RNAs (sRNAs) represent a highly diverse RNA class ranging from 8 to 200
nucleotides in length, originating from the bacterial chromosome, plasmids or phages.
After syntheses sRNAs can remain inside the bacterial cell, be secreted or packed into
outer membrane vesicles (OMV), enabling various intra- and inter-kingdom interactions.
Different sRNAs biotypes display differences in structure, mechanism of action and level
of regulation (i.e. transcription, translation, mRNA stability, etc.), but could be broadly
grouped in: trans-acting sRNAs (bind to target mRNAs) and cis-encoded sRNAs (or
antisense RNA that may interact not only with mRNAs, but also with proteins and DNA).
Even though the advancement of high-throughput sequencing technology led to a burst
of knowledge on small RNAs complexity and diversity, there are still specific challenges
related to sRNA-seq data analysis that need to be resolved. Two main challenges,
associated to short length of many bacterial sRNA biotypes, are: (i) to discriminate
between functional sRNAs synthesized by bacterial cell and degradation fragments
produced by sample preparation and (ii) to detect functional sRNAs displaying sequence
variation. While loss of very small sized sRNAs could easily be overcome by cutting-off
only the specific adapter sequences that were used in sRNA library preparation, providing
a proper mapping still remains a strenuous task.
The aim of this study was to test five different mapping tools that are widely used in NGS
data analysis (bbmap, bowtie2, bwa, minimap2 and segemehl) for their performances in
mapping of bacterial OMV sRNA-seq data to bacterial reference genome. For this test
publicly available NCBI sRNA-seq dataset from OMVs of Aliivibrio fischeri (PRJNA629425)
was used, as it contained sRNAs of different length and biotype and because A.fischeri
reference genome and annotation were available (PRJNA12986). We evaluated five
mappers using alignment and assignment rates as well as computational time. Alignment
rate was calculated as the ratio of aligned and input reads, while the assignment rate
was calculated as the ratio of assigned and aligned reads. Finally, totals of detected
sRNAs biotypes were compared between different mappers. The statistical analysis was
performed in R (version 4.3.0) and performance metrics are discussed.",
publisher = "Belgrade : Institute of molecular genetics and genetic engineering",
journal = "4th Belgrade Bioinformatics Conference",
title = "Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles",
pages = "85-85",
volume = "4",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2030"
}

Banović Đeri, B., Nešić, S., Pantelić, A., Samardžić, J.,& Nikolić, D.. (2023). Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles. in 4th Belgrade Bioinformatics Conference
Belgrade : Institute of molecular genetics and genetic engineering., 4, 85-85.
https://hdl.handle.net/21.15107/rcub_imagine_2030

Banović Đeri B, Nešić S, Pantelić A, Samardžić J, Nikolić D. Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles. in 4th Belgrade Bioinformatics Conference. 2023;4:85-85.
https://hdl.handle.net/21.15107/rcub_imagine_2030 .

Banović Đeri, Bojana, Nešić, Sofija, Pantelić, Ana, Samardžić, Jelena, Nikolić, Dragana, "Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles" in 4th Belgrade Bioinformatics Conference, 4 (2023):85-85,
https://hdl.handle.net/21.15107/rcub_imagine_2030 .

TY  - CONF
AU  - Milić, Dejana
AU  - Pantelić, Ana
AU  - Banović Đeri, Bojana
AU  - Samardžić, Jelena
AU  - Vidović, Marija
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1848
AB  - In the global warming era, we are facing extreme changes in environmental conditions such
as high and low temperatures, high light and ultraviolet radiation intensity, as well as drought
and increased CO2 levels. The effects of these factors on plants are often interrelated and usually
result in a disturbed balance between the amount of energy received and the ability to process
it. In order to balance energy input and prevent photooxidative damage, plants have evolved
multiple mechanisms for energy dissipation and photoprotection. To efficiently dissipate the excess
excitation energy (EEE), the additional electron sinks, such as photorespiration, biosynthesis
of phenolics and nitrate reduction are stimulated. Variegated leaves of Pelargonium zonale have
been proven to be a suitable model system for examining ‘source–sink’ interactions within the
same leaf, providing the same microenvironment conditions, unlike common root-shoot studies.
The aim of our study was to investigate carbon and nitrogen reallocation between photosynthetically
active (green leaf sectors) and photosynthetically inactive (white leaf sectors) under EEE
pressure induced by low temperature in combination with high light intensity. Besides the amino
acids and phenolics analyses, we monitored morphological and photosynthetic parameters of
P. zonale leaves. Our results revealed higher content of free proteogenic amino acids in the white
leaf sectors than in the green ones. Moreover, EEE triggered increased polyphenol synthesis, namely
anthocyanins, already on the fourth day of the experiment. Also, the leaf fresh/dry weight (FW/
DW) ratio was significantly lower in plants exposed to EEE, indicating possible cell wall stiffening.
PB  - Serbian Plant Physiology Society Institute for Biological Research “Siniša Stanković” – National Institute of Republic of Serbia, University of Belgrade Faculty of Biology, University of Belgrade
C3  - 4th International Conference on Plant Biology and 23rd SPPS Meeting, 2022
T1  - The role of the sink tissue in variegated Pelargonium zonale under excess excitation energy pressure morphologic, photosynthetic and metabolic study
SP  - 66
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1848
ER  - 

@conference{
author = "Milić, Dejana and Pantelić, Ana and Banović Đeri, Bojana and Samardžić, Jelena and Vidović, Marija",
year = "2022",
abstract = "In the global warming era, we are facing extreme changes in environmental conditions such
as high and low temperatures, high light and ultraviolet radiation intensity, as well as drought
and increased CO2 levels. The effects of these factors on plants are often interrelated and usually
result in a disturbed balance between the amount of energy received and the ability to process
it. In order to balance energy input and prevent photooxidative damage, plants have evolved
multiple mechanisms for energy dissipation and photoprotection. To efficiently dissipate the excess
excitation energy (EEE), the additional electron sinks, such as photorespiration, biosynthesis
of phenolics and nitrate reduction are stimulated. Variegated leaves of Pelargonium zonale have
been proven to be a suitable model system for examining ‘source–sink’ interactions within the
same leaf, providing the same microenvironment conditions, unlike common root-shoot studies.
The aim of our study was to investigate carbon and nitrogen reallocation between photosynthetically
active (green leaf sectors) and photosynthetically inactive (white leaf sectors) under EEE
pressure induced by low temperature in combination with high light intensity. Besides the amino
acids and phenolics analyses, we monitored morphological and photosynthetic parameters of
P. zonale leaves. Our results revealed higher content of free proteogenic amino acids in the white
leaf sectors than in the green ones. Moreover, EEE triggered increased polyphenol synthesis, namely
anthocyanins, already on the fourth day of the experiment. Also, the leaf fresh/dry weight (FW/
DW) ratio was significantly lower in plants exposed to EEE, indicating possible cell wall stiffening.",
publisher = "Serbian Plant Physiology Society Institute for Biological Research “Siniša Stanković” – National Institute of Republic of Serbia, University of Belgrade Faculty of Biology, University of Belgrade",
journal = "4th International Conference on Plant Biology and 23rd SPPS Meeting, 2022",
title = "The role of the sink tissue in variegated Pelargonium zonale under excess excitation energy pressure morphologic, photosynthetic and metabolic study",
pages = "66",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1848"
}

Milić, D., Pantelić, A., Banović Đeri, B., Samardžić, J.,& Vidović, M.. (2022). The role of the sink tissue in variegated Pelargonium zonale under excess excitation energy pressure morphologic, photosynthetic and metabolic study. in 4th International Conference on Plant Biology and 23rd SPPS Meeting, 2022
Serbian Plant Physiology Society Institute for Biological Research “Siniša Stanković” – National Institute of Republic of Serbia, University of Belgrade Faculty of Biology, University of Belgrade., 66.
https://hdl.handle.net/21.15107/rcub_imagine_1848

Milić D, Pantelić A, Banović Đeri B, Samardžić J, Vidović M. The role of the sink tissue in variegated Pelargonium zonale under excess excitation energy pressure morphologic, photosynthetic and metabolic study. in 4th International Conference on Plant Biology and 23rd SPPS Meeting, 2022. 2022;:66.
https://hdl.handle.net/21.15107/rcub_imagine_1848 .

Milić, Dejana, Pantelić, Ana, Banović Đeri, Bojana, Samardžić, Jelena, Vidović, Marija, "The role of the sink tissue in variegated Pelargonium zonale under excess excitation energy pressure morphologic, photosynthetic and metabolic study" in 4th International Conference on Plant Biology and 23rd SPPS Meeting, 2022 (2022):66,
https://hdl.handle.net/21.15107/rcub_imagine_1848 .

TY  - JOUR
AU  - Banović Đeri, Bojana
AU  - Bozić, Manja
AU  - Dudić, Dragana
AU  - Vicić, Ivan
AU  - Milivojević, Marija
AU  - Ignjatović-Micić, Dragana
AU  - Samardžić, Jelena
AU  - Vancetović, Jelena
AU  - Delić, Nenad
AU  - Nikolić, Ana
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1576
AB  - One of the strategies for overcoming global climate change threatening to decrease maize yield is early sowing. To contribute to the development of cold-tolerant hybrids this research focused on the genetic background's comparative analysis in maize inbreds with good combining ability. Leaf whole-transcriptome sequencing of 46 maize genotypes revealed 77 differentially expressed genes (DEGs) between Lancaster and other heterotic groups (i.e. BSSS, Iowa dent, Ohio), referred to as non-Lancaster group, under optimal growing conditions. Cold test of the subset of four Lancaster and four non-Lancaster lines showed that the former were cold sensitive and the latter cold tolerant. Cold-induced expression analysis of seven DEGs in eight lines revealed different expression regulation dependent on the duration of cold exposure and genetic background for six out of seven analysed genes-chloroplast ATP-sulphurylase, photosystem II cytochrome b559 alpha subunit, CIPK serine-threonine protein kinase 15, glutamyl-tRNA reductase, photosystem II reaction centre protein I and Calvin cycle CP12-chloroplastic-like encoding genes. The results imply that differently regulated basic processes between Lancaster and non-Lancaster maize group involve, at least, photosynthesis and sulphate assimilation, contributing to their different cold response and different adaptation to low temperatures.
PB  - Wiley, Hoboken
T2  - Journal of Agronomy and Crop Science
T1  - Leaf transcriptome analysis of Lancaster versus other heterotic groups' maize inbred lines revealed different regulation of cold-responsive genes
EP  - 509
IS  - 4
SP  - 497
VL  - 208
DO  - 10.1111/jac.12529
ER  - 

@article{
author = "Banović Đeri, Bojana and Bozić, Manja and Dudić, Dragana and Vicić, Ivan and Milivojević, Marija and Ignjatović-Micić, Dragana and Samardžić, Jelena and Vancetović, Jelena and Delić, Nenad and Nikolić, Ana",
year = "2022",
abstract = "One of the strategies for overcoming global climate change threatening to decrease maize yield is early sowing. To contribute to the development of cold-tolerant hybrids this research focused on the genetic background's comparative analysis in maize inbreds with good combining ability. Leaf whole-transcriptome sequencing of 46 maize genotypes revealed 77 differentially expressed genes (DEGs) between Lancaster and other heterotic groups (i.e. BSSS, Iowa dent, Ohio), referred to as non-Lancaster group, under optimal growing conditions. Cold test of the subset of four Lancaster and four non-Lancaster lines showed that the former were cold sensitive and the latter cold tolerant. Cold-induced expression analysis of seven DEGs in eight lines revealed different expression regulation dependent on the duration of cold exposure and genetic background for six out of seven analysed genes-chloroplast ATP-sulphurylase, photosystem II cytochrome b559 alpha subunit, CIPK serine-threonine protein kinase 15, glutamyl-tRNA reductase, photosystem II reaction centre protein I and Calvin cycle CP12-chloroplastic-like encoding genes. The results imply that differently regulated basic processes between Lancaster and non-Lancaster maize group involve, at least, photosynthesis and sulphate assimilation, contributing to their different cold response and different adaptation to low temperatures.",
publisher = "Wiley, Hoboken",
journal = "Journal of Agronomy and Crop Science",
title = "Leaf transcriptome analysis of Lancaster versus other heterotic groups' maize inbred lines revealed different regulation of cold-responsive genes",
pages = "509-497",
number = "4",
volume = "208",
doi = "10.1111/jac.12529"
}

Banović Đeri, B., Bozić, M., Dudić, D., Vicić, I., Milivojević, M., Ignjatović-Micić, D., Samardžić, J., Vancetović, J., Delić, N.,& Nikolić, A.. (2022). Leaf transcriptome analysis of Lancaster versus other heterotic groups' maize inbred lines revealed different regulation of cold-responsive genes. in Journal of Agronomy and Crop Science
Wiley, Hoboken., 208(4), 497-509.
https://doi.org/10.1111/jac.12529

Banović Đeri B, Bozić M, Dudić D, Vicić I, Milivojević M, Ignjatović-Micić D, Samardžić J, Vancetović J, Delić N, Nikolić A. Leaf transcriptome analysis of Lancaster versus other heterotic groups' maize inbred lines revealed different regulation of cold-responsive genes. in Journal of Agronomy and Crop Science. 2022;208(4):497-509.
doi:10.1111/jac.12529 .

Banović Đeri, Bojana, Bozić, Manja, Dudić, Dragana, Vicić, Ivan, Milivojević, Marija, Ignjatović-Micić, Dragana, Samardžić, Jelena, Vancetović, Jelena, Delić, Nenad, Nikolić, Ana, "Leaf transcriptome analysis of Lancaster versus other heterotic groups' maize inbred lines revealed different regulation of cold-responsive genes" in Journal of Agronomy and Crop Science, 208, no. 4 (2022):497-509,
https://doi.org/10.1111/jac.12529 . .

TY  - JOUR
AU  - Ahmadi-Teshniz, Fereshteh
AU  - Shiran, Behrouz
AU  - Mousavi-Fard, Sadegh
AU  - Fallahi, Hossein
AU  - Banović Đeri, Bojana
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1549
AB  - Background Novel strategies for improvement of ornamental plants and their properties relay on miRNA control of differential plant gene expression modulation. Still, in response to the same abiotic stresses, some conserved miRNA families show different expression patterns in different plant species. In parallel, the use of deep sequencing technologies reveals new levels of complexity of regulatory networks in plants through identification of new miRNAs. Methods and results Fritillaria imperialis plants were collected from their natural habitats in Koohrang, Chaharmahal va Bakhtiari, Iran. Several tissues including stamen, pistil, petal, sepal, leaf, stem, bulb and fruit were collected during three developmental stages (stem elongation, flower development and seed head stages). Using RNAseq and qRT-PCR approach, this research revealed 21 conserved miRNAs, matching 15 miRNA families, in Fritilaria imperialis. Conclusions The expression of seven conserved miRNAs (Fim-miR156b, Fim-miR159, Fim-miR166a-5p, Fim-miR169d-5p, Fim-miR171c, Fim-miR393 and Fim-miR396e-3p) was further investigated in different tissues and three developmental stages, suggesting different roles for these miRNAs during growth and development of crown imperial. Gained knowledge from this research can open the door to find efficient ways to secure crown imperial survival, preservation and utilization and if proven useful may be applied in other plant species as well.
PB  - Springer, Dordrecht
T2  - Molecular Biology Reports
T1  - Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing
EP  - 1132
IS  - 2
SP  - 1121
VL  - 49
DO  - 10.1007/s11033-021-06938-1
ER  - 

@article{
author = "Ahmadi-Teshniz, Fereshteh and Shiran, Behrouz and Mousavi-Fard, Sadegh and Fallahi, Hossein and Banović Đeri, Bojana",
year = "2022",
abstract = "Background Novel strategies for improvement of ornamental plants and their properties relay on miRNA control of differential plant gene expression modulation. Still, in response to the same abiotic stresses, some conserved miRNA families show different expression patterns in different plant species. In parallel, the use of deep sequencing technologies reveals new levels of complexity of regulatory networks in plants through identification of new miRNAs. Methods and results Fritillaria imperialis plants were collected from their natural habitats in Koohrang, Chaharmahal va Bakhtiari, Iran. Several tissues including stamen, pistil, petal, sepal, leaf, stem, bulb and fruit were collected during three developmental stages (stem elongation, flower development and seed head stages). Using RNAseq and qRT-PCR approach, this research revealed 21 conserved miRNAs, matching 15 miRNA families, in Fritilaria imperialis. Conclusions The expression of seven conserved miRNAs (Fim-miR156b, Fim-miR159, Fim-miR166a-5p, Fim-miR169d-5p, Fim-miR171c, Fim-miR393 and Fim-miR396e-3p) was further investigated in different tissues and three developmental stages, suggesting different roles for these miRNAs during growth and development of crown imperial. Gained knowledge from this research can open the door to find efficient ways to secure crown imperial survival, preservation and utilization and if proven useful may be applied in other plant species as well.",
publisher = "Springer, Dordrecht",
journal = "Molecular Biology Reports",
title = "Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing",
pages = "1132-1121",
number = "2",
volume = "49",
doi = "10.1007/s11033-021-06938-1"
}

Ahmadi-Teshniz, F., Shiran, B., Mousavi-Fard, S., Fallahi, H.,& Banović Đeri, B.. (2022). Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing. in Molecular Biology Reports
Springer, Dordrecht., 49(2), 1121-1132.
https://doi.org/10.1007/s11033-021-06938-1

Ahmadi-Teshniz F, Shiran B, Mousavi-Fard S, Fallahi H, Banović Đeri B. Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing. in Molecular Biology Reports. 2022;49(2):1121-1132.
doi:10.1007/s11033-021-06938-1 .

Ahmadi-Teshniz, Fereshteh, Shiran, Behrouz, Mousavi-Fard, Sadegh, Fallahi, Hossein, Banović Đeri, Bojana, "Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing" in Molecular Biology Reports, 49, no. 2 (2022):1121-1132,
https://doi.org/10.1007/s11033-021-06938-1 . .

TY  - CONF
AU  - Mladenović, Marko
AU  - Grčić, Nikola
AU  - Dudić, Dragana
AU  - Nikolić, Ana
AU  - Božić, Manja
AU  - Delić, Nenad
AU  - Prodanović, Slaven
AU  - Banović Đeri, Bojana
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1872
AB  - Multidisciplinary research is today commonly used in plant breeding for improving important agronomic
traits. High throughput genotyping technologies and genotype – phenotype association studies as widely
used for improving breeding programs, depend on bioinformatics analysis for extracting information from
the gathered data. In this research, among plethora of widely used bioinformatics approaches, the custom
made one was chosen, based on the current recommendations in the field.
The material includes a set of 46 maize inbred lines commonly used in maize breeding programs. Phenotyping
was done for thirteen important quantitative agronomic traits in 8 environments during two years (2018
and 2019). For the purpose of genotyping, plants of all inbred lines were grown under optimal conditions
and sampled after completing the V4 growth stage. Total RNA was isolated from the third leaf of three plants
per inbred line and used for cDNA preparation by Illumina TruSeq Stranded RNA LT kit. Pair-end RNA-Seq
based on Next Generation Sequencing methodology was performed on MiSeq Illumina sequencer using
MiSeq Reagent kit, v2 (2 x 150bp). Raw sequencing data of maize leaves’ transcriptionally active genome
regions at the moment of sampling were used for identification of single nucleotide polymorphisms (SNPs)
in each of 46 inbred lines.
Bioinformatics pipeline for data manipulation and analysis was custom made and included FastQC (for
quality control (QC) of raw data), Trimmomatic tool v0.32 (for adapter and contaminants removal, as well
as for the removal of regions with QC below 30), TopHat (insert size 130, standard deviation 50, maximum
intron size 100.000 – for mapping filtered reads onto the B73 maize reference genome v3.0), Cufflinks
v2.2.1 (for reads assembly), Cuffmerge (for the final transcriptome assembly) and an intersection output of
two independent SNPs calling tools FreeBayes and BCFtools (to minimize false positive results). With the
aim to find SNP markers which show strongly statistically supported relationship with favorable values of
investigated quantitative traits, genotype - phenotype association analysis was conducted. It was performed
using two approaches – one relying on the TASSEL software, widely used in agronomics and the other based
on machine learning software like WEKA, rarely used in agronomics. The results of two approaches were
compared and discussed.
PB  - Novi Sad : Faculty of Sciences, Department of Biology and Ecology
C3  - Biologia Serbica
T1  - Bioinformatics pipeline for genotyping and genotype - phenotype association study in maize (Zea mays L.)
IS  - 1 (Special Edition)
SP  - 109
VL  - 43
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1872
ER  - 

@conference{
author = "Mladenović, Marko and Grčić, Nikola and Dudić, Dragana and Nikolić, Ana and Božić, Manja and Delić, Nenad and Prodanović, Slaven and Banović Đeri, Bojana",
year = "2021",
abstract = "Multidisciplinary research is today commonly used in plant breeding for improving important agronomic
traits. High throughput genotyping technologies and genotype – phenotype association studies as widely
used for improving breeding programs, depend on bioinformatics analysis for extracting information from
the gathered data. In this research, among plethora of widely used bioinformatics approaches, the custom
made one was chosen, based on the current recommendations in the field.
The material includes a set of 46 maize inbred lines commonly used in maize breeding programs. Phenotyping
was done for thirteen important quantitative agronomic traits in 8 environments during two years (2018
and 2019). For the purpose of genotyping, plants of all inbred lines were grown under optimal conditions
and sampled after completing the V4 growth stage. Total RNA was isolated from the third leaf of three plants
per inbred line and used for cDNA preparation by Illumina TruSeq Stranded RNA LT kit. Pair-end RNA-Seq
based on Next Generation Sequencing methodology was performed on MiSeq Illumina sequencer using
MiSeq Reagent kit, v2 (2 x 150bp). Raw sequencing data of maize leaves’ transcriptionally active genome
regions at the moment of sampling were used for identification of single nucleotide polymorphisms (SNPs)
in each of 46 inbred lines.
Bioinformatics pipeline for data manipulation and analysis was custom made and included FastQC (for
quality control (QC) of raw data), Trimmomatic tool v0.32 (for adapter and contaminants removal, as well
as for the removal of regions with QC below 30), TopHat (insert size 130, standard deviation 50, maximum
intron size 100.000 – for mapping filtered reads onto the B73 maize reference genome v3.0), Cufflinks
v2.2.1 (for reads assembly), Cuffmerge (for the final transcriptome assembly) and an intersection output of
two independent SNPs calling tools FreeBayes and BCFtools (to minimize false positive results). With the
aim to find SNP markers which show strongly statistically supported relationship with favorable values of
investigated quantitative traits, genotype - phenotype association analysis was conducted. It was performed
using two approaches – one relying on the TASSEL software, widely used in agronomics and the other based
on machine learning software like WEKA, rarely used in agronomics. The results of two approaches were
compared and discussed.",
publisher = "Novi Sad : Faculty of Sciences, Department of Biology and Ecology",
journal = "Biologia Serbica",
title = "Bioinformatics pipeline for genotyping and genotype - phenotype association study in maize (Zea mays L.)",
number = "1 (Special Edition)",
pages = "109",
volume = "43",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1872"
}

Mladenović, M., Grčić, N., Dudić, D., Nikolić, A., Božić, M., Delić, N., Prodanović, S.,& Banović Đeri, B.. (2021). Bioinformatics pipeline for genotyping and genotype - phenotype association study in maize (Zea mays L.). in Biologia Serbica
Novi Sad : Faculty of Sciences, Department of Biology and Ecology., 43(1 (Special Edition)), 109.
https://hdl.handle.net/21.15107/rcub_imagine_1872

Mladenović M, Grčić N, Dudić D, Nikolić A, Božić M, Delić N, Prodanović S, Banović Đeri B. Bioinformatics pipeline for genotyping and genotype - phenotype association study in maize (Zea mays L.). in Biologia Serbica. 2021;43(1 (Special Edition)):109.
https://hdl.handle.net/21.15107/rcub_imagine_1872 .

Mladenović, Marko, Grčić, Nikola, Dudić, Dragana, Nikolić, Ana, Božić, Manja, Delić, Nenad, Prodanović, Slaven, Banović Đeri, Bojana, "Bioinformatics pipeline for genotyping and genotype - phenotype association study in maize (Zea mays L.)" in Biologia Serbica, 43, no. 1 (Special Edition) (2021):109,
https://hdl.handle.net/21.15107/rcub_imagine_1872 .

TY  - CONF
AU  - Banović Đeri, Bojana
AU  - Vidanović, Dejan
AU  - Bojana, Tešović
AU  - Petrović, Tamaš
AU  - Ristić, Danijela
AU  - Vučurović, Ivan
AU  - Dudić, Dragana
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1869
AB  - Positively oriented single stranded RNA viruses [ssRNA(+)] persistently affect health and well-being of all
eukaryotes, including plants, animals and humans (i.e. SARS-CoV-2, yellow fever, hepatitis C, zika, West Nile,
pepper mild mottle virus, etc.). How come these viruses are so wide spread and hard to eradicate? Besides
their high changeability, another major reason is their ability to mimic host processes upon entering the host.
Only recently it was revealed that ssRNA(+) viruses undergo methylation inside the host in the process that
is similar to the methylation of the hosts’ own mRNAs. Such process may enable or disable virus to avoid
some of the host’s defense mechanisms, but it inevitably impacts viral stability and fitness.
Studies on this topic have only started, opening even more questions, with major ones being: how ssRNA(+)
methylation, that occurs in the host, impacts viral pathogenicity and are these methylation patterns different
in different hosts and for different ssRNA(+) viruses or do these viral methylomes share more universal
pattern in concordance with their similar genome organization? Among numerous different methylation
patterns of RNA, this research focused on N6-methyladenosine (m6A), as the most common and abundant
methylation in eukaryotes, which was confirmed to be present in ssRNA(+) viruses as well.
This study searched for patterns in the primary sequences and secondary structures of ssRNA(+) that are
associated to m6A methylation sites relying on the experimentally obtained m6A datasets for eukaryotes and
eukaryotic ssRNA(+) viruses. The results are discussed in view of datasets characteristics and study approach.
PB  - Novi Sad : Faculty of Sciences, Department of Biology and Ecology
C3  - Biologia Serbica
T1  - Bioinformatics analysis of eukaryotic positively oriented single stranded RNA viruses
IS  - 1 (Special Edition)
SP  - 29
VL  - 43
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1869
ER  - 

@conference{
author = "Banović Đeri, Bojana and Vidanović, Dejan and Bojana, Tešović and Petrović, Tamaš and Ristić, Danijela and Vučurović, Ivan and Dudić, Dragana",
year = "2021",
abstract = "Positively oriented single stranded RNA viruses [ssRNA(+)] persistently affect health and well-being of all
eukaryotes, including plants, animals and humans (i.e. SARS-CoV-2, yellow fever, hepatitis C, zika, West Nile,
pepper mild mottle virus, etc.). How come these viruses are so wide spread and hard to eradicate? Besides
their high changeability, another major reason is their ability to mimic host processes upon entering the host.
Only recently it was revealed that ssRNA(+) viruses undergo methylation inside the host in the process that
is similar to the methylation of the hosts’ own mRNAs. Such process may enable or disable virus to avoid
some of the host’s defense mechanisms, but it inevitably impacts viral stability and fitness.
Studies on this topic have only started, opening even more questions, with major ones being: how ssRNA(+)
methylation, that occurs in the host, impacts viral pathogenicity and are these methylation patterns different
in different hosts and for different ssRNA(+) viruses or do these viral methylomes share more universal
pattern in concordance with their similar genome organization? Among numerous different methylation
patterns of RNA, this research focused on N6-methyladenosine (m6A), as the most common and abundant
methylation in eukaryotes, which was confirmed to be present in ssRNA(+) viruses as well.
This study searched for patterns in the primary sequences and secondary structures of ssRNA(+) that are
associated to m6A methylation sites relying on the experimentally obtained m6A datasets for eukaryotes and
eukaryotic ssRNA(+) viruses. The results are discussed in view of datasets characteristics and study approach.",
publisher = "Novi Sad : Faculty of Sciences, Department of Biology and Ecology",
journal = "Biologia Serbica",
title = "Bioinformatics analysis of eukaryotic positively oriented single stranded RNA viruses",
number = "1 (Special Edition)",
pages = "29",
volume = "43",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1869"
}

Banović Đeri, B., Vidanović, D., Bojana, T., Petrović, T., Ristić, D., Vučurović, I.,& Dudić, D.. (2021). Bioinformatics analysis of eukaryotic positively oriented single stranded RNA viruses. in Biologia Serbica
Novi Sad : Faculty of Sciences, Department of Biology and Ecology., 43(1 (Special Edition)), 29.
https://hdl.handle.net/21.15107/rcub_imagine_1869

Banović Đeri B, Vidanović D, Bojana T, Petrović T, Ristić D, Vučurović I, Dudić D. Bioinformatics analysis of eukaryotic positively oriented single stranded RNA viruses. in Biologia Serbica. 2021;43(1 (Special Edition)):29.
https://hdl.handle.net/21.15107/rcub_imagine_1869 .

Banović Đeri, Bojana, Vidanović, Dejan, Bojana, Tešović, Petrović, Tamaš, Ristić, Danijela, Vučurović, Ivan, Dudić, Dragana, "Bioinformatics analysis of eukaryotic positively oriented single stranded RNA viruses" in Biologia Serbica, 43, no. 1 (Special Edition) (2021):29,
https://hdl.handle.net/21.15107/rcub_imagine_1869 .

TY  - CONF
AU  - Vidović, Marija
AU  - Banović Đeri, Bojana
AU  - Samardžić, Jelena
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1873
AB  - Variegated Pelargonium zonale leaves have proven to be an excellent model system to examine source–sink
interactions within the same organ providing the equal microenvironment conditions, unlike common shoot/
root relation studies. Photosynthetically non-active (W) mesophyll cells contain smaller plastids lacking thylakoid
membranes or starch granules, and exhibit no peroxisomes in comparison to photosynthetically active
(G) cells. With the aim of gaining a deeper insight into molecular phenotype of W leaf tissue, particularly
the one related to photosynthetic-dependent H2O2 metabolism, transcriptomes of these two metabolically
contrasted tissues were compared.
High-quality total RNA from W and G leaf tissues was extracted according to our previously optimised
protocol. Highly purified cDNA libraries were synthesized and sequenced on an Illumina platform. The
ambiguous nucleotides, adapter sequences, and low-quality sequences were trimmed and the read quality
was checked before and after the trimming. In total, 39763284 (with Q30=94.3%) and 42062153 (with
Q30=94.0%) clean reads were obtained in G and W total RNA samples, respectively, and used to perform
transcriptome assembly by Trinity software. After removing the redundancy, via Corset software, 139811
transcripts with 139575 unigenes were annotated through comparison with seven commonly used databases
(NCBI non-redundant protein and nucleotide sequences; PFAM; Clusters of Orthologous Groups of proteins,
Swiss-Prot, KEGG, GO).
Analysis of differentially expressed genes was performed using DESeq2 R package and revealed 4668 upregulated
genes and 6689 down-regulated genes in G tissue compared with W one. Among the up-regulated
genes in G tissue, the majority was associated with cytoskeleton, photosynthetic processes, plastids, thylakoids
and transport, while in W tissue up-regulated genes were mainly found to encode enzymes with ATPase
activity, carbohydrate absorption and digestion, callose, pectin and linoleic acid metabolism. Moreover, a significant
difference between these two tissues differing in H2O2 generation rate was observed in the expression
level of genes involved in H2O2 scavenging. Enzymatic constituents of the ascorbate-glutathione cycle and
glutathione-S-transferase were up-regulated in W tissue, while catalase, glutathione-peroxidases and three
Class III peroxidases were all up-regulated in G tissue. The obtained transcriptome results were correlated
with previously revealed morphological, biochemical, and molecular characteristics of these two tissues.
PB  - Novi Sad : Faculty of Sciences, Department of Biology and Ecology
C3  - Biologia Serbica
T1  - Comparative De Novo Transcriptomic Analysis of Photosynthetically Active and Non-Photosynthetically Active Tissues of Variegated Pelargonium zonale Leaves
IS  - 1 (Special Edition)
SP  - 107
VL  - 43
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1873
ER  - 

@conference{
author = "Vidović, Marija and Banović Đeri, Bojana and Samardžić, Jelena",
year = "2021",
abstract = "Variegated Pelargonium zonale leaves have proven to be an excellent model system to examine source–sink
interactions within the same organ providing the equal microenvironment conditions, unlike common shoot/
root relation studies. Photosynthetically non-active (W) mesophyll cells contain smaller plastids lacking thylakoid
membranes or starch granules, and exhibit no peroxisomes in comparison to photosynthetically active
(G) cells. With the aim of gaining a deeper insight into molecular phenotype of W leaf tissue, particularly
the one related to photosynthetic-dependent H2O2 metabolism, transcriptomes of these two metabolically
contrasted tissues were compared.
High-quality total RNA from W and G leaf tissues was extracted according to our previously optimised
protocol. Highly purified cDNA libraries were synthesized and sequenced on an Illumina platform. The
ambiguous nucleotides, adapter sequences, and low-quality sequences were trimmed and the read quality
was checked before and after the trimming. In total, 39763284 (with Q30=94.3%) and 42062153 (with
Q30=94.0%) clean reads were obtained in G and W total RNA samples, respectively, and used to perform
transcriptome assembly by Trinity software. After removing the redundancy, via Corset software, 139811
transcripts with 139575 unigenes were annotated through comparison with seven commonly used databases
(NCBI non-redundant protein and nucleotide sequences; PFAM; Clusters of Orthologous Groups of proteins,
Swiss-Prot, KEGG, GO).
Analysis of differentially expressed genes was performed using DESeq2 R package and revealed 4668 upregulated
genes and 6689 down-regulated genes in G tissue compared with W one. Among the up-regulated
genes in G tissue, the majority was associated with cytoskeleton, photosynthetic processes, plastids, thylakoids
and transport, while in W tissue up-regulated genes were mainly found to encode enzymes with ATPase
activity, carbohydrate absorption and digestion, callose, pectin and linoleic acid metabolism. Moreover, a significant
difference between these two tissues differing in H2O2 generation rate was observed in the expression
level of genes involved in H2O2 scavenging. Enzymatic constituents of the ascorbate-glutathione cycle and
glutathione-S-transferase were up-regulated in W tissue, while catalase, glutathione-peroxidases and three
Class III peroxidases were all up-regulated in G tissue. The obtained transcriptome results were correlated
with previously revealed morphological, biochemical, and molecular characteristics of these two tissues.",
publisher = "Novi Sad : Faculty of Sciences, Department of Biology and Ecology",
journal = "Biologia Serbica",
title = "Comparative De Novo Transcriptomic Analysis of Photosynthetically Active and Non-Photosynthetically Active Tissues of Variegated Pelargonium zonale Leaves",
number = "1 (Special Edition)",
pages = "107",
volume = "43",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1873"
}

Vidović, M., Banović Đeri, B.,& Samardžić, J.. (2021). Comparative De Novo Transcriptomic Analysis of Photosynthetically Active and Non-Photosynthetically Active Tissues of Variegated Pelargonium zonale Leaves. in Biologia Serbica
Novi Sad : Faculty of Sciences, Department of Biology and Ecology., 43(1 (Special Edition)), 107.
https://hdl.handle.net/21.15107/rcub_imagine_1873

Vidović M, Banović Đeri B, Samardžić J. Comparative De Novo Transcriptomic Analysis of Photosynthetically Active and Non-Photosynthetically Active Tissues of Variegated Pelargonium zonale Leaves. in Biologia Serbica. 2021;43(1 (Special Edition)):107.
https://hdl.handle.net/21.15107/rcub_imagine_1873 .

Vidović, Marija, Banović Đeri, Bojana, Samardžić, Jelena, "Comparative De Novo Transcriptomic Analysis of Photosynthetically Active and Non-Photosynthetically Active Tissues of Variegated Pelargonium zonale Leaves" in Biologia Serbica, 43, no. 1 (Special Edition) (2021):107,
https://hdl.handle.net/21.15107/rcub_imagine_1873 .

TY  - CONF
AU  - Božić, Manja
AU  - Nikolić, Ana
AU  - Dudić, Dragana
AU  - Ignjatović-Micić, Dragana
AU  - Samardžić, Jelena
AU  - Delić, Nenad
AU  - Banović Đeri, Bojana
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1874
AB  - Finding new ways of improving crop quality, yield potential and abiotic stress tolerance are some of the most
important pursuits in crop production today. As one of the biggest causes of yield and productivity reduction
is climate change, specifically increasing temperatures and drought during the summer, a large number of
strategies is focussed on lessening their negative effects. Cropping pattern changes include earlier sowing
(early spring), when the temperatures are lower, as one of the most promising escape strategies for avoiding
high summer temperatures. Thus, development of cold tolerant maize lines became an important goal.
Comparative analysis of 46 maize inbred lines belonging to two different genetic backgrounds, one predominantly
cold tolerante (marked as Non-Lancaster) and the other predominantly cold sensitive (marked as
Lancaster) in the field, was done by whole transriptome sequencing and differential gene expression (DGE)
analysis. Plants were grown under optimal, greenhouse conditions and sampled after completing the V4
growth stage. Total RNA isolated from leaves of three plants per inbred line was used for cDNA library preparation
by Illumina TruSeq Stranded RNA LT kit. Pair-end sequencing was performed on MiSeq Illumina
sequencer using MiSeq Reagent kit, v2 (2 x 150bp). Data manipulation and analysis was performed using a
custom-made bioinformatics pipeline that included high throughput sequence data quality control (using
FastQC), removal of low quality reads (using Trimmomatic tool, version 0.32), transcriptome assembly and
mapping (using Cufflinks, version 2.2.1), expression quantification (using CuffDiff) and DGE analysis (using
BLAST2GO and GO analysis Toolkit and Database for Agricultural Community, agriGO v2).
DGE analysis revealed 77 differentially expressed genes (DEGs) between the Lancaster and the Non-Lancaster
group, 21 of which were statistically supported for differential expression between the two groups and
annotated as involved in abiotic stress responses in maize and other plant species. To test DEGs response to
cold stress expression of a subset of seven DEGs in eight inbred lines (4 belonging to Lancaster and 4 belonging
to Non-Lancaster genetic background) was analyzed under 24h long exposure to low temperatures (6/4°
C, 12h photoperiod), with sampling being done 6h and 24h after beginning of the treatment, as well as after
48h of recovery. Six DEGs showed different expression regulation dependent on cold exposure duration and
genetic background. These findings imply differently regulated processes between the analysed Lancaster
and Non-Lancaster inbred lines, contributing to their different cold response and adaptation, and will be
further used for the development of cold tolerant hybrids.
PB  - Novi Sad : Faculty of Sciences, Department of Biology and Ecology
C3  - Biologia Serbica
T1  - Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature
IS  - 1 (Special Edition)
SP  - 106
VL  - 43
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1874
ER  - 

@conference{
author = "Božić, Manja and Nikolić, Ana and Dudić, Dragana and Ignjatović-Micić, Dragana and Samardžić, Jelena and Delić, Nenad and Banović Đeri, Bojana",
year = "2021",
abstract = "Finding new ways of improving crop quality, yield potential and abiotic stress tolerance are some of the most
important pursuits in crop production today. As one of the biggest causes of yield and productivity reduction
is climate change, specifically increasing temperatures and drought during the summer, a large number of
strategies is focussed on lessening their negative effects. Cropping pattern changes include earlier sowing
(early spring), when the temperatures are lower, as one of the most promising escape strategies for avoiding
high summer temperatures. Thus, development of cold tolerant maize lines became an important goal.
Comparative analysis of 46 maize inbred lines belonging to two different genetic backgrounds, one predominantly
cold tolerante (marked as Non-Lancaster) and the other predominantly cold sensitive (marked as
Lancaster) in the field, was done by whole transriptome sequencing and differential gene expression (DGE)
analysis. Plants were grown under optimal, greenhouse conditions and sampled after completing the V4
growth stage. Total RNA isolated from leaves of three plants per inbred line was used for cDNA library preparation
by Illumina TruSeq Stranded RNA LT kit. Pair-end sequencing was performed on MiSeq Illumina
sequencer using MiSeq Reagent kit, v2 (2 x 150bp). Data manipulation and analysis was performed using a
custom-made bioinformatics pipeline that included high throughput sequence data quality control (using
FastQC), removal of low quality reads (using Trimmomatic tool, version 0.32), transcriptome assembly and
mapping (using Cufflinks, version 2.2.1), expression quantification (using CuffDiff) and DGE analysis (using
BLAST2GO and GO analysis Toolkit and Database for Agricultural Community, agriGO v2).
DGE analysis revealed 77 differentially expressed genes (DEGs) between the Lancaster and the Non-Lancaster
group, 21 of which were statistically supported for differential expression between the two groups and
annotated as involved in abiotic stress responses in maize and other plant species. To test DEGs response to
cold stress expression of a subset of seven DEGs in eight inbred lines (4 belonging to Lancaster and 4 belonging
to Non-Lancaster genetic background) was analyzed under 24h long exposure to low temperatures (6/4°
C, 12h photoperiod), with sampling being done 6h and 24h after beginning of the treatment, as well as after
48h of recovery. Six DEGs showed different expression regulation dependent on cold exposure duration and
genetic background. These findings imply differently regulated processes between the analysed Lancaster
and Non-Lancaster inbred lines, contributing to their different cold response and adaptation, and will be
further used for the development of cold tolerant hybrids.",
publisher = "Novi Sad : Faculty of Sciences, Department of Biology and Ecology",
journal = "Biologia Serbica",
title = "Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature",
number = "1 (Special Edition)",
pages = "106",
volume = "43",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1874"
}

Božić, M., Nikolić, A., Dudić, D., Ignjatović-Micić, D., Samardžić, J., Delić, N.,& Banović Đeri, B.. (2021). Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature. in Biologia Serbica
Novi Sad : Faculty of Sciences, Department of Biology and Ecology., 43(1 (Special Edition)), 106.
https://hdl.handle.net/21.15107/rcub_imagine_1874

Božić M, Nikolić A, Dudić D, Ignjatović-Micić D, Samardžić J, Delić N, Banović Đeri B. Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature. in Biologia Serbica. 2021;43(1 (Special Edition)):106.
https://hdl.handle.net/21.15107/rcub_imagine_1874 .

Božić, Manja, Nikolić, Ana, Dudić, Dragana, Ignjatović-Micić, Dragana, Samardžić, Jelena, Delić, Nenad, Banović Đeri, Bojana, "Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature" in Biologia Serbica, 43, no. 1 (Special Edition) (2021):106,
https://hdl.handle.net/21.15107/rcub_imagine_1874 .

TY  - JOUR
AU  - Vidanović, Dejan
AU  - Tesović, Bojana
AU  - Volkening, Jeremy D.
AU  - Afonso, Claudio L.
AU  - Quick, Joshua
AU  - Sekler, Milanko
AU  - Knezević, Aleksandra
AU  - Janković, Marko
AU  - Jovanović, Tanja
AU  - Petrović, Tamas
AU  - Banović Đeri, Bojana
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1453
AB  - This study was endeavoured to contribute in furthering our understanding of the molecular epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by sequencing and analysing the first full-length genome sequences obtained from 48 coronavirus disease-2019 (COVID-19) patients in five districts in Western Serbia in the period April 2020-July 2020. SARS-CoV-2 sequences in Western Serbia distinguished from the Wuhan sequence in 128 SNPs in total. The phylogenetic structure of local SARS-CoV-2 isolates suggested the existence of at least four distinct groups of SARS-CoV-2 strains in Western Serbia. The first group is the most similar to the strain from Italy. These isolates included two 20A sequences and 15-30 20B sequences that displayed a newly occurring set of four conjoined mutations. The second group is the most similar to the strain from France, carrying two mutations and belonged to 20A clade. The third group is the most similar to the strain from Switzerland carrying four co-occurring mutations and belonging to 20B clade. The fourth group is the most similar to another strain from France, displaying one mutation that gave rise to a single local isolate that belonged to 20A clade.
PB  - Cambridge Univ Press, New York
T2  - Epidemiology and Infection
T1  - First whole-genome analysis of the novel coronavirus (SARS-CoV-2) obtained from COVID-19 patients from five districts in Western Serbia
VL  - 149
DO  - 10.1017/S095026882100220X
ER  - 

@article{
author = "Vidanović, Dejan and Tesović, Bojana and Volkening, Jeremy D. and Afonso, Claudio L. and Quick, Joshua and Sekler, Milanko and Knezević, Aleksandra and Janković, Marko and Jovanović, Tanja and Petrović, Tamas and Banović Đeri, Bojana",
year = "2021",
abstract = "This study was endeavoured to contribute in furthering our understanding of the molecular epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by sequencing and analysing the first full-length genome sequences obtained from 48 coronavirus disease-2019 (COVID-19) patients in five districts in Western Serbia in the period April 2020-July 2020. SARS-CoV-2 sequences in Western Serbia distinguished from the Wuhan sequence in 128 SNPs in total. The phylogenetic structure of local SARS-CoV-2 isolates suggested the existence of at least four distinct groups of SARS-CoV-2 strains in Western Serbia. The first group is the most similar to the strain from Italy. These isolates included two 20A sequences and 15-30 20B sequences that displayed a newly occurring set of four conjoined mutations. The second group is the most similar to the strain from France, carrying two mutations and belonged to 20A clade. The third group is the most similar to the strain from Switzerland carrying four co-occurring mutations and belonging to 20B clade. The fourth group is the most similar to another strain from France, displaying one mutation that gave rise to a single local isolate that belonged to 20A clade.",
publisher = "Cambridge Univ Press, New York",
journal = "Epidemiology and Infection",
title = "First whole-genome analysis of the novel coronavirus (SARS-CoV-2) obtained from COVID-19 patients from five districts in Western Serbia",
volume = "149",
doi = "10.1017/S095026882100220X"
}

Vidanović, D., Tesović, B., Volkening, J. D., Afonso, C. L., Quick, J., Sekler, M., Knezević, A., Janković, M., Jovanović, T., Petrović, T.,& Banović Đeri, B.. (2021). First whole-genome analysis of the novel coronavirus (SARS-CoV-2) obtained from COVID-19 patients from five districts in Western Serbia. in Epidemiology and Infection
Cambridge Univ Press, New York., 149.
https://doi.org/10.1017/S095026882100220X

Vidanović D, Tesović B, Volkening JD, Afonso CL, Quick J, Sekler M, Knezević A, Janković M, Jovanović T, Petrović T, Banović Đeri B. First whole-genome analysis of the novel coronavirus (SARS-CoV-2) obtained from COVID-19 patients from five districts in Western Serbia. in Epidemiology and Infection. 2021;149.
doi:10.1017/S095026882100220X .

Vidanović, Dejan, Tesović, Bojana, Volkening, Jeremy D., Afonso, Claudio L., Quick, Joshua, Sekler, Milanko, Knezević, Aleksandra, Janković, Marko, Jovanović, Tanja, Petrović, Tamas, Banović Đeri, Bojana, "First whole-genome analysis of the novel coronavirus (SARS-CoV-2) obtained from COVID-19 patients from five districts in Western Serbia" in Epidemiology and Infection, 149 (2021),
https://doi.org/10.1017/S095026882100220X . .

TY  - JOUR
AU  - Ugrin, Milena
AU  - Dinić, Jelena
AU  - Jeremić, Sanja
AU  - Dragičević, Sandra
AU  - Banović Đeri, Bojana
AU  - Nikolić, Aleksandra
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1478
AB  - Bacterial nanocellulose (BNC) stands out among polymers as a promising biomaterial due to its mechanical strength, hydrophilicity, biocompatibility, biodegradability, low toxicity and renewability. The use of scaffolds based on BNC for 3D cell culture has been previously demonstrated. The study exploited excellent properties of the BNC to develop an efficient and low-cost in vitro cell migration assay. The BNC scaffold was introduced into a cell culture 24 h after the SW480 cells were seeded, and cells were allowed to enter the scaffold within the next 24-48 h. The cells were stained with different fluorophores either before or after the introduction of the scaffold in the culture. Untreated cells were observed to enter the BNC scaffold in significant numbers, form clusters and retain a high viability after 48 h. To validate the assay's usability for drug development, the treatments of SW480 cells were performed using aspirin, an agent known to reduce the migratory potential of this cell line in culture. This study demonstrates the application of BNC as a scaffold for cell migration testing as a low-cost alternative to commercial assays based on the Boyden chamber principle. The assay could be further developed for routine use in cancer research and anticancer drug development.
PB  - MDPI, Basel
T2  - Nanomaterials
T1  - Bacterial Nanocellulose as a Scaffold for In Vitro Cell Migration Assay
IS  - 9
VL  - 11
DO  - 10.3390/nano11092322
ER  - 

@article{
author = "Ugrin, Milena and Dinić, Jelena and Jeremić, Sanja and Dragičević, Sandra and Banović Đeri, Bojana and Nikolić, Aleksandra",
year = "2021",
abstract = "Bacterial nanocellulose (BNC) stands out among polymers as a promising biomaterial due to its mechanical strength, hydrophilicity, biocompatibility, biodegradability, low toxicity and renewability. The use of scaffolds based on BNC for 3D cell culture has been previously demonstrated. The study exploited excellent properties of the BNC to develop an efficient and low-cost in vitro cell migration assay. The BNC scaffold was introduced into a cell culture 24 h after the SW480 cells were seeded, and cells were allowed to enter the scaffold within the next 24-48 h. The cells were stained with different fluorophores either before or after the introduction of the scaffold in the culture. Untreated cells were observed to enter the BNC scaffold in significant numbers, form clusters and retain a high viability after 48 h. To validate the assay's usability for drug development, the treatments of SW480 cells were performed using aspirin, an agent known to reduce the migratory potential of this cell line in culture. This study demonstrates the application of BNC as a scaffold for cell migration testing as a low-cost alternative to commercial assays based on the Boyden chamber principle. The assay could be further developed for routine use in cancer research and anticancer drug development.",
publisher = "MDPI, Basel",
journal = "Nanomaterials",
title = "Bacterial Nanocellulose as a Scaffold for In Vitro Cell Migration Assay",
number = "9",
volume = "11",
doi = "10.3390/nano11092322"
}

Ugrin, M., Dinić, J., Jeremić, S., Dragičević, S., Banović Đeri, B.,& Nikolić, A.. (2021). Bacterial Nanocellulose as a Scaffold for In Vitro Cell Migration Assay. in Nanomaterials
MDPI, Basel., 11(9).
https://doi.org/10.3390/nano11092322

Ugrin M, Dinić J, Jeremić S, Dragičević S, Banović Đeri B, Nikolić A. Bacterial Nanocellulose as a Scaffold for In Vitro Cell Migration Assay. in Nanomaterials. 2021;11(9).
doi:10.3390/nano11092322 .

Ugrin, Milena, Dinić, Jelena, Jeremić, Sanja, Dragičević, Sandra, Banović Đeri, Bojana, Nikolić, Aleksandra, "Bacterial Nanocellulose as a Scaffold for In Vitro Cell Migration Assay" in Nanomaterials, 11, no. 9 (2021),
https://doi.org/10.3390/nano11092322 . .

TY  - CHAP
AU  - Miljuš-Đukić, Jovanka
AU  - Banović Đeri, Bojana
AU  - Leal Filho, Walter
AU  - Azul, Anabela Marisa
AU  - Brandli, Luciana
AU  - Lange Salvia, Amanda
AU  - Wall, Tony
PY  - 2020
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1645
PB  - Springer International Publishing
T2  - Life on Land
T2  - Life on Land
T1  - Genetically Modified Organisms (GMOs)
EP  - 14
SP  - 1
DO  - 10.1007/978-3-319-71065-5_54-1
ER  - 

@inbook{
author = "Miljuš-Đukić, Jovanka and Banović Đeri, Bojana and Leal Filho, Walter and Azul, Anabela Marisa and Brandli, Luciana and Lange Salvia, Amanda and Wall, Tony",
year = "2020",
publisher = "Springer International Publishing",
journal = "Life on Land, Life on Land",
booktitle = "Genetically Modified Organisms (GMOs)",
pages = "14-1",
doi = "10.1007/978-3-319-71065-5_54-1"
}

Miljuš-Đukić, J., Banović Đeri, B., Leal Filho, W., Azul, A. M., Brandli, L., Lange Salvia, A.,& Wall, T.. (2020). Genetically Modified Organisms (GMOs). in Life on Land
Springer International Publishing., 1-14.
https://doi.org/10.1007/978-3-319-71065-5_54-1

Miljuš-Đukić J, Banović Đeri B, Leal Filho W, Azul AM, Brandli L, Lange Salvia A, Wall T. Genetically Modified Organisms (GMOs). in Life on Land. 2020;:1-14.
doi:10.1007/978-3-319-71065-5_54-1 .

Miljuš-Đukić, Jovanka, Banović Đeri, Bojana, Leal Filho, Walter, Azul, Anabela Marisa, Brandli, Luciana, Lange Salvia, Amanda, Wall, Tony, "Genetically Modified Organisms (GMOs)" in Life on Land (2020):1-14,
https://doi.org/10.1007/978-3-319-71065-5_54-1 . .

TY  - CHAP
AU  - Miljuš-Đukić, Jovanka
AU  - Banović Đeri, Bojana
AU  - Leal Filho, Walter
AU  - Azul, Anabela Marisa
AU  - Brandli, Luciana
AU  - Lange Salvia, Amanda
AU  - Wall, Tony
PY  - 2020
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1644
PB  - Springer International Publishing
T2  - Life on Land
T2  - Life on Land
T1  - Impact Caused by Genetically Modified Organisms (GMOs)
EP  - 13
SP  - 1
DO  - 10.1007/978-3-319-71065-5_55-1
ER  - 

@inbook{
author = "Miljuš-Đukić, Jovanka and Banović Đeri, Bojana and Leal Filho, Walter and Azul, Anabela Marisa and Brandli, Luciana and Lange Salvia, Amanda and Wall, Tony",
year = "2020",
publisher = "Springer International Publishing",
journal = "Life on Land, Life on Land",
booktitle = "Impact Caused by Genetically Modified Organisms (GMOs)",
pages = "13-1",
doi = "10.1007/978-3-319-71065-5_55-1"
}

Miljuš-Đukić, J., Banović Đeri, B., Leal Filho, W., Azul, A. M., Brandli, L., Lange Salvia, A.,& Wall, T.. (2020). Impact Caused by Genetically Modified Organisms (GMOs). in Life on Land
Springer International Publishing., 1-13.
https://doi.org/10.1007/978-3-319-71065-5_55-1

Miljuš-Đukić J, Banović Đeri B, Leal Filho W, Azul AM, Brandli L, Lange Salvia A, Wall T. Impact Caused by Genetically Modified Organisms (GMOs). in Life on Land. 2020;:1-13.
doi:10.1007/978-3-319-71065-5_55-1 .

Miljuš-Đukić, Jovanka, Banović Đeri, Bojana, Leal Filho, Walter, Azul, Anabela Marisa, Brandli, Luciana, Lange Salvia, Amanda, Wall, Tony, "Impact Caused by Genetically Modified Organisms (GMOs)" in Life on Land (2020):1-13,
https://doi.org/10.1007/978-3-319-71065-5_55-1 . .

TY  - JOUR
AU  - Shahvali, Roohollah
AU  - Shiran, Behrouz
AU  - Ravash, Rudabeh
AU  - Fallahi, Hossein
AU  - Banović Đeri, Bojana
PY  - 2020
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1308
AB  - Genus Prunus is of great importance for cultivation, mainly because its main species provide fruits and seeds, valuable ornamental qualifies and timber. However, stone fruit trees and almonds, major cultivars of genus Prunus, are sensitive to salt stress. Such sensitivity causes losses in stone fruit and almond production (ca. 50% of regular yield at high salinity grounds). Having in mind that symbiosis with arbuscular mycorrhiza fungi (AMF) may improve plant tolerance to salt stress and that symbiosis effect should be tested in case-by-case approach, we tested salt stress response of AMF inoculated GF677 rootstock (Prunus dulcis x Prunus persica hybrid) in this study. Adding to that, we tested GF677 symbiosis with two AMF species R. intraradices and F. mosseae. Results showed that under salinity stress AMF inoculated GF677 plants displayed improved physiological parameters (chlorophyll, soluble sugars and proline content) and increased antioxidant enzymes activity in comparison to non-inoculated control plants. Comparison of two AMF species beneficial effects on tested parameters revealed that for total chlorophyll content inoculation with F. mosseae has prevailed, while for total soluble sugars and proline content R. intraradices has prevailed. Finally, GF677 in symbiosis with F. mosseae was selected for molecular studies of salinity response. Since many of plants' genes involved in simultaneous response to salt stress and AMF colonization remained unidentified so far, we performed bioinformatics analysis of freely online available data to find differentially expressed genes common to these two responses. Upon GO classification and networking analysis of genes identified as common to both responses, we selected two most prominent ones (UDPGT73C6 and CYP707A3) and tested their expression profile in leaves and roots of F. mosseae inoculated GF677 rootstocks under salt stress. Even though specific roles of UDPGT73C6 and CYP707A3 are un-characterized in Prunus tree species, results suggested their involvement in response to salt stress and AMF inoculation of GF677 plants, which is in concordance with a scarce knowledge on their roles in other plant species. Based on this study finding we may conclude that symbiosis of GF677 rootstocks with AMF increases plants tolerance to salinity stress, which should be considered in other Prunus tree species as well.
PB  - Elsevier, Amsterdam
T2  - Scientia Horticulturae
T1  - Effect of symbiosis with arbuscular mycorrhizal fungi on salt stress tolerance in GF677 (peach x almond) rootstock
VL  - 272
DO  - 10.1016/j.scienta.2020.109535
ER  - 

@article{
author = "Shahvali, Roohollah and Shiran, Behrouz and Ravash, Rudabeh and Fallahi, Hossein and Banović Đeri, Bojana",
year = "2020",
abstract = "Genus Prunus is of great importance for cultivation, mainly because its main species provide fruits and seeds, valuable ornamental qualifies and timber. However, stone fruit trees and almonds, major cultivars of genus Prunus, are sensitive to salt stress. Such sensitivity causes losses in stone fruit and almond production (ca. 50% of regular yield at high salinity grounds). Having in mind that symbiosis with arbuscular mycorrhiza fungi (AMF) may improve plant tolerance to salt stress and that symbiosis effect should be tested in case-by-case approach, we tested salt stress response of AMF inoculated GF677 rootstock (Prunus dulcis x Prunus persica hybrid) in this study. Adding to that, we tested GF677 symbiosis with two AMF species R. intraradices and F. mosseae. Results showed that under salinity stress AMF inoculated GF677 plants displayed improved physiological parameters (chlorophyll, soluble sugars and proline content) and increased antioxidant enzymes activity in comparison to non-inoculated control plants. Comparison of two AMF species beneficial effects on tested parameters revealed that for total chlorophyll content inoculation with F. mosseae has prevailed, while for total soluble sugars and proline content R. intraradices has prevailed. Finally, GF677 in symbiosis with F. mosseae was selected for molecular studies of salinity response. Since many of plants' genes involved in simultaneous response to salt stress and AMF colonization remained unidentified so far, we performed bioinformatics analysis of freely online available data to find differentially expressed genes common to these two responses. Upon GO classification and networking analysis of genes identified as common to both responses, we selected two most prominent ones (UDPGT73C6 and CYP707A3) and tested their expression profile in leaves and roots of F. mosseae inoculated GF677 rootstocks under salt stress. Even though specific roles of UDPGT73C6 and CYP707A3 are un-characterized in Prunus tree species, results suggested their involvement in response to salt stress and AMF inoculation of GF677 plants, which is in concordance with a scarce knowledge on their roles in other plant species. Based on this study finding we may conclude that symbiosis of GF677 rootstocks with AMF increases plants tolerance to salinity stress, which should be considered in other Prunus tree species as well.",
publisher = "Elsevier, Amsterdam",
journal = "Scientia Horticulturae",
title = "Effect of symbiosis with arbuscular mycorrhizal fungi on salt stress tolerance in GF677 (peach x almond) rootstock",
volume = "272",
doi = "10.1016/j.scienta.2020.109535"
}

Shahvali, R., Shiran, B., Ravash, R., Fallahi, H.,& Banović Đeri, B.. (2020). Effect of symbiosis with arbuscular mycorrhizal fungi on salt stress tolerance in GF677 (peach x almond) rootstock. in Scientia Horticulturae
Elsevier, Amsterdam., 272.
https://doi.org/10.1016/j.scienta.2020.109535

Shahvali R, Shiran B, Ravash R, Fallahi H, Banović Đeri B. Effect of symbiosis with arbuscular mycorrhizal fungi on salt stress tolerance in GF677 (peach x almond) rootstock. in Scientia Horticulturae. 2020;272.
doi:10.1016/j.scienta.2020.109535 .

Shahvali, Roohollah, Shiran, Behrouz, Ravash, Rudabeh, Fallahi, Hossein, Banović Đeri, Bojana, "Effect of symbiosis with arbuscular mycorrhizal fungi on salt stress tolerance in GF677 (peach x almond) rootstock" in Scientia Horticulturae, 272 (2020),
https://doi.org/10.1016/j.scienta.2020.109535 . .

TY  - JOUR
AU  - Eshaghi, Mahsa
AU  - Shiran, Behrouz
AU  - Fallahi, Hossein
AU  - Ravash, Rudabeh
AU  - Banović Đeri, Bojana
PY  - 2019
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1218
AB  - Crown imperial (CI) has been used in traditional medicine. Today it is known that such beneficial effects are due to its richness in steroidal alkaloids (SA). Using de novo transcriptomics, orthologues/paralogues finder, phylogenetic analysis and tissue- and developmental stage-specific expression analysis, we identified ten genes and several TFs involved in the biosynthesis of SA in CI. The comparative analysis of ten genes expression profiles revealed the possibility of their co-regulation, which may imply the possibility of their organization in metabolic gene clusters. Having in mind convergent evolution of steroidal biosynthetic pathways in flowering plants and records of convergent evolution of specific proteins, observed expression patterns open a reasonable interest to investigate the possibility of the existence of genes cluster organization in SA pathway in the family Liliaceae or at least in some species of genus Fritillaria. Obtained results support transcriptomics as useful approach in elucidating genes underlying complex biochemical pathways.
PB  - Academic Press Inc Elsevier Science, San Diego
T2  - Genomics
T1  - Identification of genes involved in steroid alkaloid biosynthesis in Fritillaria imperialis via de novo transcriptomics
EP  - 1372
IS  - 6
SP  - 1360
VL  - 111
DO  - 10.1016/j.ygeno.2018.09.008
ER  - 

@article{
author = "Eshaghi, Mahsa and Shiran, Behrouz and Fallahi, Hossein and Ravash, Rudabeh and Banović Đeri, Bojana",
year = "2019",
abstract = "Crown imperial (CI) has been used in traditional medicine. Today it is known that such beneficial effects are due to its richness in steroidal alkaloids (SA). Using de novo transcriptomics, orthologues/paralogues finder, phylogenetic analysis and tissue- and developmental stage-specific expression analysis, we identified ten genes and several TFs involved in the biosynthesis of SA in CI. The comparative analysis of ten genes expression profiles revealed the possibility of their co-regulation, which may imply the possibility of their organization in metabolic gene clusters. Having in mind convergent evolution of steroidal biosynthetic pathways in flowering plants and records of convergent evolution of specific proteins, observed expression patterns open a reasonable interest to investigate the possibility of the existence of genes cluster organization in SA pathway in the family Liliaceae or at least in some species of genus Fritillaria. Obtained results support transcriptomics as useful approach in elucidating genes underlying complex biochemical pathways.",
publisher = "Academic Press Inc Elsevier Science, San Diego",
journal = "Genomics",
title = "Identification of genes involved in steroid alkaloid biosynthesis in Fritillaria imperialis via de novo transcriptomics",
pages = "1372-1360",
number = "6",
volume = "111",
doi = "10.1016/j.ygeno.2018.09.008"
}

Eshaghi, M., Shiran, B., Fallahi, H., Ravash, R.,& Banović Đeri, B.. (2019). Identification of genes involved in steroid alkaloid biosynthesis in Fritillaria imperialis via de novo transcriptomics. in Genomics
Academic Press Inc Elsevier Science, San Diego., 111(6), 1360-1372.
https://doi.org/10.1016/j.ygeno.2018.09.008

Eshaghi M, Shiran B, Fallahi H, Ravash R, Banović Đeri B. Identification of genes involved in steroid alkaloid biosynthesis in Fritillaria imperialis via de novo transcriptomics. in Genomics. 2019;111(6):1360-1372.
doi:10.1016/j.ygeno.2018.09.008 .

Eshaghi, Mahsa, Shiran, Behrouz, Fallahi, Hossein, Ravash, Rudabeh, Banović Đeri, Bojana, "Identification of genes involved in steroid alkaloid biosynthesis in Fritillaria imperialis via de novo transcriptomics" in Genomics, 111, no. 6 (2019):1360-1372,
https://doi.org/10.1016/j.ygeno.2018.09.008 . .

TY  - JOUR
AU  - Jantsch, Michael F.
AU  - Quattrone, Alessandro
AU  - O'Connell, Mary
AU  - Helm, Mark
AU  - Frye, Michaela
AU  - Macias-Gonzales, Manuel
AU  - Ohman, Marie
AU  - Ameres, Stefan
AU  - Willems, Luc
AU  - Fuks, Francois
AU  - Oulas, Anastasis
AU  - Vanacova, Stepanka
AU  - Nielsen, Henrik
AU  - Bousquet-Antonelli, Cecile
AU  - Motorin, Yuri
AU  - Roignant, Jean-Yves
AU  - Balatsos, Nikolaos
AU  - Dinnyes, Andras
AU  - Baranov, Pavel
AU  - Kelly, Vincent
AU  - Lamm, Ayelet
AU  - Rechavi, Gideon
AU  - Pelizzola, Mattia
AU  - Liepins, Janis
AU  - Kholodnyuk, Irina Holodnuka
AU  - Zammit, Vanessa
AU  - Ayers, Duncan
AU  - Drablos, Finn
AU  - Dahl, John Arne
AU  - Bujnicki, Janusz
AU  - Jeronimo, Carmen
AU  - Almeida, Raquel
AU  - Neagu, Monica
AU  - Costache, Marieta
AU  - Banković, Jasna
AU  - Banović Đeri, Bojana
AU  - Kyselovic, Jan
AU  - Valor, Luis Miguel
AU  - Selbert, Stefan
AU  - Pir, Pinar
AU  - Demircan, Turan
AU  - Cowling, Victoria
AU  - Schaefer, Matthias
AU  - Rossmanith, Walter
AU  - Lafontaine, Denis
AU  - David, Alexandre
AU  - Carre, Clement
AU  - Lyko, Frank
AU  - Schaffrath, Raffael
AU  - Schwartz, Schraga
AU  - Verdel, Andre
AU  - Klungland, Arne
AU  - Purta, Elzbieta
AU  - Timotijević, Gordana
AU  - Cardona, Fernando
AU  - Davalos, Alberto
AU  - Ballana, Ester
AU  - O'Carroll, Donal
AU  - Ule, Jernej
AU  - Fray, Rupert
PY  - 2018
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1100
AB  - The genetic alphabet consists of the four letters: C, A, G, and T in DNA and C,A,G, and U in RNA. Triplets of these four letters jointly encode 20 different amino acids out of which proteins of all organisms are built. This system is universal and is found in all kingdoms of life. However, bases in DNA and RNA can be chemically modified. In DNA, around 10 different modifications are known, and those have been studied intensively over the past 20years. Scientific studies on DNA modifications and proteins that recognize them gave rise to the large field of epigenetic and epigenomic research. The outcome of this intense research field is the discovery that development, ageing, and stem-cell dependent regeneration but also several diseases including cancer are largely controlled by the epigenetic state of cells. Consequently, this research has already led to the first FDA approved drugs that exploit the gained knowledge to combat disease. In recent years, the similar to 150 modifications found in RNA have come to the focus of intense research. Here we provide a perspective on necessary and expected developments in the fast expanding area of RNA modifications, termed epitranscriptomics.
PB  - Taylor & Francis Inc, Philadelphia
T2  - RNA Biology
T1  - Positioning Europe for the EPITRANSCRIPTOMICS challenge
EP  - 831
IS  - 6
SP  - 829
VL  - 15
DO  - 10.1080/15476286.2018.1460996
ER  - 

@article{
author = "Jantsch, Michael F. and Quattrone, Alessandro and O'Connell, Mary and Helm, Mark and Frye, Michaela and Macias-Gonzales, Manuel and Ohman, Marie and Ameres, Stefan and Willems, Luc and Fuks, Francois and Oulas, Anastasis and Vanacova, Stepanka and Nielsen, Henrik and Bousquet-Antonelli, Cecile and Motorin, Yuri and Roignant, Jean-Yves and Balatsos, Nikolaos and Dinnyes, Andras and Baranov, Pavel and Kelly, Vincent and Lamm, Ayelet and Rechavi, Gideon and Pelizzola, Mattia and Liepins, Janis and Kholodnyuk, Irina Holodnuka and Zammit, Vanessa and Ayers, Duncan and Drablos, Finn and Dahl, John Arne and Bujnicki, Janusz and Jeronimo, Carmen and Almeida, Raquel and Neagu, Monica and Costache, Marieta and Banković, Jasna and Banović Đeri, Bojana and Kyselovic, Jan and Valor, Luis Miguel and Selbert, Stefan and Pir, Pinar and Demircan, Turan and Cowling, Victoria and Schaefer, Matthias and Rossmanith, Walter and Lafontaine, Denis and David, Alexandre and Carre, Clement and Lyko, Frank and Schaffrath, Raffael and Schwartz, Schraga and Verdel, Andre and Klungland, Arne and Purta, Elzbieta and Timotijević, Gordana and Cardona, Fernando and Davalos, Alberto and Ballana, Ester and O'Carroll, Donal and Ule, Jernej and Fray, Rupert",
year = "2018",
abstract = "The genetic alphabet consists of the four letters: C, A, G, and T in DNA and C,A,G, and U in RNA. Triplets of these four letters jointly encode 20 different amino acids out of which proteins of all organisms are built. This system is universal and is found in all kingdoms of life. However, bases in DNA and RNA can be chemically modified. In DNA, around 10 different modifications are known, and those have been studied intensively over the past 20years. Scientific studies on DNA modifications and proteins that recognize them gave rise to the large field of epigenetic and epigenomic research. The outcome of this intense research field is the discovery that development, ageing, and stem-cell dependent regeneration but also several diseases including cancer are largely controlled by the epigenetic state of cells. Consequently, this research has already led to the first FDA approved drugs that exploit the gained knowledge to combat disease. In recent years, the similar to 150 modifications found in RNA have come to the focus of intense research. Here we provide a perspective on necessary and expected developments in the fast expanding area of RNA modifications, termed epitranscriptomics.",
publisher = "Taylor & Francis Inc, Philadelphia",
journal = "RNA Biology",
title = "Positioning Europe for the EPITRANSCRIPTOMICS challenge",
pages = "831-829",
number = "6",
volume = "15",
doi = "10.1080/15476286.2018.1460996"
}

Jantsch, M. F., Quattrone, A., O'Connell, M., Helm, M., Frye, M., Macias-Gonzales, M., Ohman, M., Ameres, S., Willems, L., Fuks, F., Oulas, A., Vanacova, S., Nielsen, H., Bousquet-Antonelli, C., Motorin, Y., Roignant, J., Balatsos, N., Dinnyes, A., Baranov, P., Kelly, V., Lamm, A., Rechavi, G., Pelizzola, M., Liepins, J., Kholodnyuk, I. H., Zammit, V., Ayers, D., Drablos, F., Dahl, J. A., Bujnicki, J., Jeronimo, C., Almeida, R., Neagu, M., Costache, M., Banković, J., Banović Đeri, B., Kyselovic, J., Valor, L. M., Selbert, S., Pir, P., Demircan, T., Cowling, V., Schaefer, M., Rossmanith, W., Lafontaine, D., David, A., Carre, C., Lyko, F., Schaffrath, R., Schwartz, S., Verdel, A., Klungland, A., Purta, E., Timotijević, G., Cardona, F., Davalos, A., Ballana, E., O'Carroll, D., Ule, J.,& Fray, R.. (2018). Positioning Europe for the EPITRANSCRIPTOMICS challenge. in RNA Biology
Taylor & Francis Inc, Philadelphia., 15(6), 829-831.
https://doi.org/10.1080/15476286.2018.1460996

Jantsch MF, Quattrone A, O'Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A, Vanacova S, Nielsen H, Bousquet-Antonelli C, Motorin Y, Roignant J, Balatsos N, Dinnyes A, Baranov P, Kelly V, Lamm A, Rechavi G, Pelizzola M, Liepins J, Kholodnyuk IH, Zammit V, Ayers D, Drablos F, Dahl JA, Bujnicki J, Jeronimo C, Almeida R, Neagu M, Costache M, Banković J, Banović Đeri B, Kyselovic J, Valor LM, Selbert S, Pir P, Demircan T, Cowling V, Schaefer M, Rossmanith W, Lafontaine D, David A, Carre C, Lyko F, Schaffrath R, Schwartz S, Verdel A, Klungland A, Purta E, Timotijević G, Cardona F, Davalos A, Ballana E, O'Carroll D, Ule J, Fray R. Positioning Europe for the EPITRANSCRIPTOMICS challenge. in RNA Biology. 2018;15(6):829-831.
doi:10.1080/15476286.2018.1460996 .

Jantsch, Michael F., Quattrone, Alessandro, O'Connell, Mary, Helm, Mark, Frye, Michaela, Macias-Gonzales, Manuel, Ohman, Marie, Ameres, Stefan, Willems, Luc, Fuks, Francois, Oulas, Anastasis, Vanacova, Stepanka, Nielsen, Henrik, Bousquet-Antonelli, Cecile, Motorin, Yuri, Roignant, Jean-Yves, Balatsos, Nikolaos, Dinnyes, Andras, Baranov, Pavel, Kelly, Vincent, Lamm, Ayelet, Rechavi, Gideon, Pelizzola, Mattia, Liepins, Janis, Kholodnyuk, Irina Holodnuka, Zammit, Vanessa, Ayers, Duncan, Drablos, Finn, Dahl, John Arne, Bujnicki, Janusz, Jeronimo, Carmen, Almeida, Raquel, Neagu, Monica, Costache, Marieta, Banković, Jasna, Banović Đeri, Bojana, Kyselovic, Jan, Valor, Luis Miguel, Selbert, Stefan, Pir, Pinar, Demircan, Turan, Cowling, Victoria, Schaefer, Matthias, Rossmanith, Walter, Lafontaine, Denis, David, Alexandre, Carre, Clement, Lyko, Frank, Schaffrath, Raffael, Schwartz, Schraga, Verdel, Andre, Klungland, Arne, Purta, Elzbieta, Timotijević, Gordana, Cardona, Fernando, Davalos, Alberto, Ballana, Ester, O'Carroll, Donal, Ule, Jernej, Fray, Rupert, "Positioning Europe for the EPITRANSCRIPTOMICS challenge" in RNA Biology, 15, no. 6 (2018):829-831,
https://doi.org/10.1080/15476286.2018.1460996 . .

TY  - JOUR
AU  - Banović Đeri, Bojana
AU  - Pajić, Vesna
AU  - Dudić, Dragana
PY  - 2018
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1191
AB  - Primary goals of 21st century science involve eco-friendly solutions for detection, control and suppression of plant viruses. Even though we are accumulating knowledge and data on plant viruses' nucleotide sequences, we are still using a minimum of information available from the collected data. Applying bioinformatics tools and data mining approach to viral sequences is extremely useful in revealing the hidden knowledge, giving guidelines for further biological/bioinformatics studies and developing novel environmental-friendly virus specific defense strategies in crop protection. In this paper we tested to what extent modern bioinformatics methods are able to reveal new information that would bring us closer to our primary goals. On the date of the search (March 2015) we extracted all available PMMoV entries from publically available databases, represented by heterogeneous data set containing 231 nucleotide sequences covering different parts of the PMMoV genome, that were of different geographical origin, related to different time periods, associated with different pathotypes, and were not previously compared to each other. Results revealed that nucleotide content at genomic positions 552, 565, 639, 666, 708, 5921, 5975 and 6002 can be used to discern three distinct PMMoV genotype variants and their association to one of two virus pathotypes, P-1,P-2 or P-1,P-2,P-3. These sites have never been reported as informative before, probably because by being silent mutations they escaped usual research scrutiny of looking for pathotype determinants among nonsense, missense mutations and indels. Our model was further tested in predicting pathotype of ten newly deposited PMMoV sequences and the successful outcome of the test supported the model as an useful asset for discrimination among pathotypes P-1,P-2 and P-1,P-2,P-3 according to distinct nucleotide content in replicase and coat protein encoding genes. Based on the presented results, we also suggested new tests for fast and cost-effective screening of PMMoV pathotypes and eventually for inducing plant resistance against pepper mild mottle virus.
PB  - Elsevier Sci Ltd, Oxford
T2  - Crop Protection
T1  - Revealing new information from existing genomic data for pepper mild mottle virus pathotype determination
EP  - 103
SP  - 93
VL  - 107
DO  - 10.1016/j.cropro.2018.01.017
ER  - 

@article{
author = "Banović Đeri, Bojana and Pajić, Vesna and Dudić, Dragana",
year = "2018",
abstract = "Primary goals of 21st century science involve eco-friendly solutions for detection, control and suppression of plant viruses. Even though we are accumulating knowledge and data on plant viruses' nucleotide sequences, we are still using a minimum of information available from the collected data. Applying bioinformatics tools and data mining approach to viral sequences is extremely useful in revealing the hidden knowledge, giving guidelines for further biological/bioinformatics studies and developing novel environmental-friendly virus specific defense strategies in crop protection. In this paper we tested to what extent modern bioinformatics methods are able to reveal new information that would bring us closer to our primary goals. On the date of the search (March 2015) we extracted all available PMMoV entries from publically available databases, represented by heterogeneous data set containing 231 nucleotide sequences covering different parts of the PMMoV genome, that were of different geographical origin, related to different time periods, associated with different pathotypes, and were not previously compared to each other. Results revealed that nucleotide content at genomic positions 552, 565, 639, 666, 708, 5921, 5975 and 6002 can be used to discern three distinct PMMoV genotype variants and their association to one of two virus pathotypes, P-1,P-2 or P-1,P-2,P-3. These sites have never been reported as informative before, probably because by being silent mutations they escaped usual research scrutiny of looking for pathotype determinants among nonsense, missense mutations and indels. Our model was further tested in predicting pathotype of ten newly deposited PMMoV sequences and the successful outcome of the test supported the model as an useful asset for discrimination among pathotypes P-1,P-2 and P-1,P-2,P-3 according to distinct nucleotide content in replicase and coat protein encoding genes. Based on the presented results, we also suggested new tests for fast and cost-effective screening of PMMoV pathotypes and eventually for inducing plant resistance against pepper mild mottle virus.",
publisher = "Elsevier Sci Ltd, Oxford",
journal = "Crop Protection",
title = "Revealing new information from existing genomic data for pepper mild mottle virus pathotype determination",
pages = "103-93",
volume = "107",
doi = "10.1016/j.cropro.2018.01.017"
}

Banović Đeri, B., Pajić, V.,& Dudić, D.. (2018). Revealing new information from existing genomic data for pepper mild mottle virus pathotype determination. in Crop Protection
Elsevier Sci Ltd, Oxford., 107, 93-103.
https://doi.org/10.1016/j.cropro.2018.01.017

Banović Đeri B, Pajić V, Dudić D. Revealing new information from existing genomic data for pepper mild mottle virus pathotype determination. in Crop Protection. 2018;107:93-103.
doi:10.1016/j.cropro.2018.01.017 .

Banović Đeri, Bojana, Pajić, Vesna, Dudić, Dragana, "Revealing new information from existing genomic data for pepper mild mottle virus pathotype determination" in Crop Protection, 107 (2018):93-103,
https://doi.org/10.1016/j.cropro.2018.01.017 . .

TY  - JOUR
AU  - Aleksić, Jelena M.
AU  - Banović Đeri, Bojana
AU  - Miljuš-Đukić, Jovanka
AU  - Jovanović, Živko
AU  - Mikić, Aleksandar
AU  - Cupina, Branko
AU  - Zlatković, Bojan
AU  - Anđelković, Snežana
AU  - Spanu, Ilaria
AU  - Jelić, Mihailo
AU  - Maksimović, Vesna R.
PY  - 2015
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/834
AB  - Although more than 400 microsatellite loci are currently available for Vicia faba L. (faba bean), an important food and feed grain crop legume, they have not yet been used for comprehensive molecular characterization of this crop. We report a three-step procedure for rapid and cost-effective delineation and utilization of informative genomic nuclear SSRs for paralleled genotyping in faba bean suitable also for other species: (i) pre-selection of loci generating PCR products of expected lengths which are potentially polymorphic (achieved by PCR amplification in bulked samples); (ii) exclusion of loci burdened with persistent null alleles and multilocus amplification products (based on PCR amplification of pre-selected loci in individual genotypes), and (iii) multiplexing. We demonstrate also that genomic SSRs are promising molecular tools for molecular characterization of faba bean required also for crop improvement.
PB  - Czech Academy Agricultural Sciences, Prague
T2  - Czech Journal of Genetics and Plant Breeding
T1  - A Rapid and Cost-effective Procedure for Delineation and Utilization of Genomic Microsatellites for Paralleled Genotyping in Vicia faba
EP  - 39
IS  - 1
SP  - 36
VL  - 51
DO  - 10.17221/153/2014-CJGPB
ER  - 

@article{
author = "Aleksić, Jelena M. and Banović Đeri, Bojana and Miljuš-Đukić, Jovanka and Jovanović, Živko and Mikić, Aleksandar and Cupina, Branko and Zlatković, Bojan and Anđelković, Snežana and Spanu, Ilaria and Jelić, Mihailo and Maksimović, Vesna R.",
year = "2015",
abstract = "Although more than 400 microsatellite loci are currently available for Vicia faba L. (faba bean), an important food and feed grain crop legume, they have not yet been used for comprehensive molecular characterization of this crop. We report a three-step procedure for rapid and cost-effective delineation and utilization of informative genomic nuclear SSRs for paralleled genotyping in faba bean suitable also for other species: (i) pre-selection of loci generating PCR products of expected lengths which are potentially polymorphic (achieved by PCR amplification in bulked samples); (ii) exclusion of loci burdened with persistent null alleles and multilocus amplification products (based on PCR amplification of pre-selected loci in individual genotypes), and (iii) multiplexing. We demonstrate also that genomic SSRs are promising molecular tools for molecular characterization of faba bean required also for crop improvement.",
publisher = "Czech Academy Agricultural Sciences, Prague",
journal = "Czech Journal of Genetics and Plant Breeding",
title = "A Rapid and Cost-effective Procedure for Delineation and Utilization of Genomic Microsatellites for Paralleled Genotyping in Vicia faba",
pages = "39-36",
number = "1",
volume = "51",
doi = "10.17221/153/2014-CJGPB"
}

Aleksić, J. M., Banović Đeri, B., Miljuš-Đukić, J., Jovanović, Ž., Mikić, A., Cupina, B., Zlatković, B., Anđelković, S., Spanu, I., Jelić, M.,& Maksimović, V. R.. (2015). A Rapid and Cost-effective Procedure for Delineation and Utilization of Genomic Microsatellites for Paralleled Genotyping in Vicia faba. in Czech Journal of Genetics and Plant Breeding
Czech Academy Agricultural Sciences, Prague., 51(1), 36-39.
https://doi.org/10.17221/153/2014-CJGPB

Aleksić JM, Banović Đeri B, Miljuš-Đukić J, Jovanović Ž, Mikić A, Cupina B, Zlatković B, Anđelković S, Spanu I, Jelić M, Maksimović VR. A Rapid and Cost-effective Procedure for Delineation and Utilization of Genomic Microsatellites for Paralleled Genotyping in Vicia faba. in Czech Journal of Genetics and Plant Breeding. 2015;51(1):36-39.
doi:10.17221/153/2014-CJGPB .

Aleksić, Jelena M., Banović Đeri, Bojana, Miljuš-Đukić, Jovanka, Jovanović, Živko, Mikić, Aleksandar, Cupina, Branko, Zlatković, Bojan, Anđelković, Snežana, Spanu, Ilaria, Jelić, Mihailo, Maksimović, Vesna R., "A Rapid and Cost-effective Procedure for Delineation and Utilization of Genomic Microsatellites for Paralleled Genotyping in Vicia faba" in Czech Journal of Genetics and Plant Breeding, 51, no. 1 (2015):36-39,
https://doi.org/10.17221/153/2014-CJGPB . .

TY  - JOUR
AU  - Aleksić, Jelena M.
AU  - Miljuš-Đukić, Jovanka
AU  - Jovanović, Živko
AU  - Tomić, Branko
AU  - Banović Đeri, Bojana
PY  - 2014
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/732
AB  - We performed in silico PCR analyses utilizing complete mitochondrial (mtDNA) genome sequences of faba bean (Vicia faba) and two related species, Vigna angularis and Vigna radiata, currently available in GenBank, to infer whether 15 published universal primer pairs for amplification of all 14 cis-spliced introns in genes of NADH subunits (nad genes) are suitable for V. faba and related species. Then, we tested via PCR reactions whether seven out of 15 primer pairs would generate PCR products suitable for further manipulation in 16 genotypes of V. faba representing all botanical varieties of this species (major, minor, equina and subsp. paucijuga) of various levels of improvement (traditional and improved cultivars) originating from Europe, Africa, Asia and south America. We provide new PCR primers for amplification of nad1 intron 2/3 in V. faba, and demonstrate intraspecific variability in primary nucleotide sequences at this locus. Based on outcomes of both in silico predictions and PCR amplification, we report a set of PCR primers for amplification of five introns in nad genes that are promising molecular tools for future phylogeographic and other studies in this species for which unambiguous data on wild ancestors, centre of origin and domestication are lacking.
PB  - Društvo genetičara Srbije, Beograd
T2  - Genetika-Belgrade
T1  - Molecular tools for utilization of mitochondrial diversity in faba bean (vicia faba)
EP  - 762
IS  - 3
SP  - 745
VL  - 46
DO  - 10.2298/GENSR1403745A
ER  - 

@article{
author = "Aleksić, Jelena M. and Miljuš-Đukić, Jovanka and Jovanović, Živko and Tomić, Branko and Banović Đeri, Bojana",
year = "2014",
abstract = "We performed in silico PCR analyses utilizing complete mitochondrial (mtDNA) genome sequences of faba bean (Vicia faba) and two related species, Vigna angularis and Vigna radiata, currently available in GenBank, to infer whether 15 published universal primer pairs for amplification of all 14 cis-spliced introns in genes of NADH subunits (nad genes) are suitable for V. faba and related species. Then, we tested via PCR reactions whether seven out of 15 primer pairs would generate PCR products suitable for further manipulation in 16 genotypes of V. faba representing all botanical varieties of this species (major, minor, equina and subsp. paucijuga) of various levels of improvement (traditional and improved cultivars) originating from Europe, Africa, Asia and south America. We provide new PCR primers for amplification of nad1 intron 2/3 in V. faba, and demonstrate intraspecific variability in primary nucleotide sequences at this locus. Based on outcomes of both in silico predictions and PCR amplification, we report a set of PCR primers for amplification of five introns in nad genes that are promising molecular tools for future phylogeographic and other studies in this species for which unambiguous data on wild ancestors, centre of origin and domestication are lacking.",
publisher = "Društvo genetičara Srbije, Beograd",
journal = "Genetika-Belgrade",
title = "Molecular tools for utilization of mitochondrial diversity in faba bean (vicia faba)",
pages = "762-745",
number = "3",
volume = "46",
doi = "10.2298/GENSR1403745A"
}

Aleksić, J. M., Miljuš-Đukić, J., Jovanović, Ž., Tomić, B.,& Banović Đeri, B.. (2014). Molecular tools for utilization of mitochondrial diversity in faba bean (vicia faba). in Genetika-Belgrade
Društvo genetičara Srbije, Beograd., 46(3), 745-762.
https://doi.org/10.2298/GENSR1403745A

Aleksić JM, Miljuš-Đukić J, Jovanović Ž, Tomić B, Banović Đeri B. Molecular tools for utilization of mitochondrial diversity in faba bean (vicia faba). in Genetika-Belgrade. 2014;46(3):745-762.
doi:10.2298/GENSR1403745A .

Aleksić, Jelena M., Miljuš-Đukić, Jovanka, Jovanović, Živko, Tomić, Branko, Banović Đeri, Bojana, "Molecular tools for utilization of mitochondrial diversity in faba bean (vicia faba)" in Genetika-Belgrade, 46, no. 3 (2014):745-762,
https://doi.org/10.2298/GENSR1403745A . .